bench/configs/cases.yaml

cases:
- case_name: KaiB
  tier: 1
  classification: known-state
  query_source_db: UniProt
  query_accession: Q79V61
  query_organism: Thermosynechococcus vestitus BP-1 (a.k.a. T. elongatus)
  canonical_query_sequence: RKTYVLKLYVAGNTPNSVRALKTLNNILEKEFKGVYALKVIDVLKNPQLAEEDKILATPTLAKVLPPPVRRIIGDLSNREKVLIGLDLLYE
  canonical_query_length: 91
  canonical_query_frame: 2QKE chain B residue numbering, residues 5..95 (matches AF-Cluster
    repo 91-aa KaiB_TE query). Protocol §2.1 initially listed 108 — the AF-Cluster
    repo (data_sep2022/00_KaiB/2qkeE.pdb + 2QKEE_colabfold.a3m) uses this 91-aa trimmed
    construct. [V5 resolved; repo pin trumps the 108-aa paper text.]
  construct_start: 5
  construct_end: 95
  states:
  - name: state_A_ground
    pdb_id: 2QKE
    chain_id: B
    residue_range: 5..95 (of 1..108 crystal residues)
    has_mutations: false
    notes: Ground-state βαββααβ KaiBTE. 2QKE has 6 chains (A-F); chain B is the only
      complete 1..108 monomer (all others have missing terminal residues). Trimmed
      to 5..95 to match AF-Cluster repo working construct.
    qc:
      method: x-ray diffraction
      resolution_A: 2.7
      n_models: 1
      chains_all:
      - A
      - B
      - C
      - D
      - E
      - F
      chain_used: B
      chains_dropped:
      - A
      - C
      - D
      - E
      - F
      missing_residues: []
      mutations_vs_canonical: []
      b_factor_mean: 97.64
      heteroatoms_removed:
      - HOH
  - name: state_B_foldswitch
    pdb_id: 5JYT
    chain_id: A
    residue_range: 5..95 (of 1..106 crystal residues)
    has_mutations: true
    notes: 'FS-state thioredoxin-like (βαβαββα). 5JYT is a stabilized KaiBTE variant:
      point mutations Y8A, N29A, G89A, D91R, Y94A (per RCSB REMARKs & paper p.839)
      plus C-terminal tags. Trimmed to 5..95 to exclude the MAPL N-tag and the DYKDDDDK
      FLAG tag.'
    qc:
      method: solution nmr
      resolution_A: null
      n_models: 20
      chains_all:
      - A
      chain_used: A
      chains_dropped: []
      missing_residues:
      - 107
      - 108
      mutations_vs_canonical:
      - - 8
        - Y
        - A
      - - 29
        - N
        - A
      - - 89
        - G
        - A
      - - 91
        - D
        - R
      - - 94
        - Y
        - A
      - - 100
        - Q
        - Y
      - - 101
        - A
        - K
      - - 102
        - E
        - D
      - - 105
        - L
        - D
      - - 106
        - G
        - K
      b_factor_mean: 0.0
      heteroatoms_removed: []
- case_name: GA_GB
  tier: 1
  classification: known-state
  query_source_db: engineered (refs. 49, 50, 51)
  query_accession: see_state_notes
  query_organism: engineered from Streptococcus protein G GB1/GA domain + HSA-binding
    GA domain
  canonical_query_sequence: TTYKLILNLKQAKEEAIKELVDAGTAEKYFKLIANAKTVEGVWTLKDEIKTFTVTE
  canonical_query_length: 56
  canonical_query_frame: 1..56 (representative = GA98 / 2LHC sequence)
  construct_start: 1
  construct_end: 56
  states:
  - name: GAWT
    pdb_id: null
    chain_id: null
    residue_range: 1..56
    has_mutations: false
    notes: 'Sequence-only variant from the AF-Cluster notebook / papers. No deposited
      PDB found in RCSB for this exact sequence. Sequence: MEAVDANSLAQAKEAAIKELKQYGIGDYYIKLINNAKTVEGVESLKNEILKALPTE'
    qc: null
  - name: GA77
    pdb_id: null
    chain_id: null
    residue_range: 1..56
    has_mutations: false
    notes: 'Sequence-only variant from the AF-Cluster notebook / papers. No deposited
      PDB found in RCSB for this exact sequence. Sequence: TTYKLILNLKQAKEEAIKELVDAGIAEKYIKLIANAKTVEGVWTLKDEILKATVTE'
    qc: null
  - name: GA88
    pdb_id: 2JWS
    chain_id: A
    residue_range: 1..56
    has_mutations: false
    notes: 'Designed variant in the GA/GB convergence series (refs. 49–51). Sequence:
      TTYKLILNLKQAKEEAIKELVDAGIAEKYIKLIANAKTVEGVWTLKDEILTFTVTE'
    qc:
      method: solution nmr
      resolution_A: null
      n_models: 20
      chains_all:
      - A
      chain_used: A
      chains_dropped: []
      missing_residues: []
      mutations_vs_canonical: []
      b_factor_mean: 0.0
      heteroatoms_removed: []
  - name: GA91
    pdb_id: null
    chain_id: null
    residue_range: 1..56
    has_mutations: false
    notes: 'Sequence-only variant from the AF-Cluster notebook / papers. No deposited
      PDB found in RCSB for this exact sequence. Sequence: TTYKLILNLKQAKEEAIKELVDAGTAEKYIKLIANAKTVEGVWTLKDEILTFTVTE'
    qc: null
  - name: GA95
    pdb_id: 2KDL
    chain_id: A
    residue_range: 1..56
    has_mutations: false
    notes: 'Designed variant in the GA/GB convergence series (refs. 49–51). Sequence:
      TTYKLILNLKQAKEEAIKELVDAGTAEKYIKLIANAKTVEGVWTLKDEIKTFTVTE'
    qc:
      method: solution nmr
      resolution_A: null
      n_models: 20
      chains_all:
      - A
      chain_used: A
      chains_dropped: []
      missing_residues: []
      mutations_vs_canonical: []
      b_factor_mean: 0.0
      heteroatoms_removed: []
  - name: GA98
    pdb_id: 2LHC
    chain_id: A
    residue_range: 1..56
    has_mutations: false
    notes: 'Designed variant in the GA/GB convergence series (refs. 49–51). Sequence:
      TTYKLILNLKQAKEEAIKELVDAGTAEKYFKLIANAKTVEGVWTLKDEIKTFTVTE'
    qc:
      method: solution nmr
      resolution_A: null
      n_models: 20
      chains_all:
      - A
      chain_used: A
      chains_dropped: []
      missing_residues: []
      mutations_vs_canonical: []
      b_factor_mean: 0.0
      heteroatoms_removed: []
  - name: GB98
    pdb_id: 2LHD
    chain_id: A
    residue_range: 1..56
    has_mutations: false
    notes: 'Designed variant in the GA/GB convergence series (refs. 49–51). Sequence:
      TTYKLILNLKQAKEEAIKELVDAGTAEKYFKLIANAKTVEGVWTYKDEIKTFTVTE'
    qc:
      method: solution nmr
      resolution_A: null
      n_models: 20
      chains_all:
      - A
      chain_used: A
      chains_dropped: []
      missing_residues: []
      mutations_vs_canonical: []
      b_factor_mean: 0.0
      heteroatoms_removed: []
  - name: GB98_T25I
    pdb_id: 2LHG
    chain_id: A
    residue_range: 1..56
    has_mutations: false
    notes: 'Designed variant in the GA/GB convergence series (refs. 49–51). Sequence:
      TTYKLILNLKQAKEEAIKELVDAGIAEKYFKLIANAKTVEGVWTYKDEIKTFTVTE'
    qc:
      method: solution nmr
      resolution_A: null
      n_models: 10
      chains_all:
      - A
      chain_used: A
      chains_dropped: []
      missing_residues: []
      mutations_vs_canonical: []
      b_factor_mean: 0.0
      heteroatoms_removed: []
  - name: GB98_T25I_L20A
    pdb_id: 2LHE
    chain_id: A
    residue_range: 1..56
    has_mutations: false
    notes: 'Designed variant in the GA/GB convergence series (refs. 49–51). Sequence:
      TTYKLILNLKQAKEEAIKEAVDAGIAEKYFKLIANAKTVEGVWTYKDEIKTFTVTE'
    qc:
      method: solution nmr
      resolution_A: null
      n_models: 20
      chains_all:
      - A
      chain_used: A
      chains_dropped: []
      missing_residues: []
      mutations_vs_canonical: []
      b_factor_mean: 0.0
      heteroatoms_removed: []
  - name: GB95
    pdb_id: 2KDM
    chain_id: A
    residue_range: 1..56
    has_mutations: false
    notes: 'Designed variant in the GA/GB convergence series (refs. 49–51). Sequence:
      TTYKLILNLKQAKEEAIKEAVDAGTAEKYFKLIANAKTVEGVWTYKDEIKTFTVTE'
    qc:
      method: solution nmr
      resolution_A: null
      n_models: 20
      chains_all:
      - A
      chain_used: A
      chains_dropped: []
      missing_residues: []
      mutations_vs_canonical: []
      b_factor_mean: 0.0
      heteroatoms_removed: []
  - name: GB91
    pdb_id: null
    chain_id: null
    residue_range: 1..56
    has_mutations: false
    notes: 'Sequence-only variant from the AF-Cluster notebook / papers. No deposited
      PDB found in RCSB for this exact sequence. Sequence: TTYKLILNLKQAKEEAIKEAVDAGTAEKYFKLYANAKTVEGVWTYKDEIKTFTVTE'
    qc: null
  - name: GB88
    pdb_id: null
    chain_id: null
    residue_range: 1..56
    has_mutations: false
    notes: 'Sequence-only variant from the AF-Cluster notebook / papers. No deposited
      PDB found in RCSB for this exact sequence. Sequence: TTYKLILNLKQAKEEAITEAVDAGTAEKYFKLYANAKTVEGVWTYKDEIKTFTVTE'
    qc: null
  - name: GB77
    pdb_id: null
    chain_id: null
    residue_range: 1..56
    has_mutations: false
    notes: 'Sequence-only variant from the AF-Cluster notebook / papers. No deposited
      PDB found in RCSB for this exact sequence. Sequence: TTYKLILNGKQLKEEAITEAVDAATAEKYFKLYANAKTVEGVWTYKDETKTFTVTE'
    qc: null
  - name: GBWT
    pdb_id: null
    chain_id: null
    residue_range: 1..56
    has_mutations: false
    notes: 'Sequence-only variant from the AF-Cluster notebook / papers. No deposited
      PDB found in RCSB for this exact sequence. Sequence: MTYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE'
    qc: null
  note: 'There are 14 sequences in the AF-Cluster notebook (12 engineered mutants
    + GAWT + GBWT). Of these, 7 have deposited RCSB structures: 2LHC (GA98), 2LHD
    (GB98), 2LHE (GB98_T25I_L20A), 2LHG (GB98_T25I), 2JWS (GA88), 2KDL (GA95), 2KDM
    (GB95). The other 7 are sequence-only variants. 2JWU (a deposited 2008 PNAS precursor)
    has a different sequence from the notebook-GB91 (the notebook explicitly flags
    `# error in Fig. 2 PNAS 2009`) — it is kept under legacy_2JWU.pdb for traceability
    but not used as a primary reference.'
- case_name: Mpt53
  tier: 2
  classification: discovery
  query_source_db: UniProt
  query_accession: P9WG65
  query_organism: Mycobacterium tuberculosis H37Rv
  canonical_query_sequence: ADERLQFTATTLSGAPFDGASLQGKPAVLWFWTPWCPFCNAEAPSLSQVAAANPAVTFVGIATRADVGAMQSFVSKYNLNFTNLNDADGVIWARYNVPWQPAFVFYRADGTSTFVNNPTAAMSQDELSGRVAALTS
  canonical_query_length: 136
  canonical_query_frame: UniProt 38..173 (mature protein, signal peptide 1..37 cleaved).
    This exactly matches the AF-Cluster repo 1LU4A_REF.a3m query (136 aa).
  construct_start: 38
  construct_end: 173
  states:
  - name: state_A_reference
    pdb_id: 1LU4
    chain_id: A
    residue_range: 1001..1134 (crystal numbering; = UniProt 38..171). 2 C-term residues
      (TS, UniProt 172–173) not in the crystal.
    has_mutations: false
    notes: Thioredoxin-like reduced state crystal structure of Mpt53. Residue numbering
      in 1LU4.pdb starts at 1001; subtract 963 to map to UniProt.
    qc:
      method: x-ray diffraction
      resolution_A: 1.12
      n_models: 1
      chains_all:
      - A
      chain_used: A
      chains_dropped: []
      missing_residues:
      - 1135
      - 1136
      mutations_vs_canonical: []
      b_factor_mean: 13.82
      heteroatoms_removed:
      - HOH
  - name: dali_best_info_only
    pdb_id: 3EMX
    chain_id: A
    residue_range: 224..347 (fragment of parent Aeropyrum pernix protein)
    has_mutations: false
    notes: DALI best hit to the predicted alternative state (per AF-Cluster Fig. 5).
      Not a direct evaluation reference; supplied for information only. Discovery-case
      §9.2 metrics only use 1LU4.
    qc:
      method: x-ray diffraction
      resolution_A: 2.25
      n_models: 1
      chains_all:
      - A
      - B
      chain_used: A
      chains_dropped:
      - B
      missing_residues: []
      mutations_vs_canonical: []
      b_factor_mean: 25.13
      heteroatoms_removed:
      - HOH
# ── Phase VIII new cases ────────────────────────────────────────────────────
- case_name: RfaH
  tier: 1
  classification: known-state
  query_source_db: UniProt
  query_accession: P0AFZ3
  query_organism: Escherichia coli K-12
  # VERIFY: fetch canonical sequence from UniProt P0AFZ3 before AF2 runs
  canonical_query_sequence: SEE_UNIPROT_P0AFZ3
  canonical_query_length: 162
  canonical_query_frame: UniProt 1..162 (full-length; NTD residues 1-100 + CTD residues 101-162)
  construct_start: 1
  construct_end: 162
  biology: >
    RfaH is a transcription elongation factor (NusG paralog). Its C-terminal
    domain (CTD, residues ~101-162) undergoes a dramatic fold-switch between a
    beta-barrel (free/NusG-like autoinhibited form) and an alpha-helical hairpin
    (when engaging the RNA polymerase NTD). The NTD (residues 1-100) is stable
    in both states. This is one of the best-characterised natural fold-switching
    proteins and a canonical Phase VIII benchmark target.
  states:
  - name: state_A_NusG_like
    # VERIFY: confirm PDB 5OND contains full-length autoinhibited RfaH before use
    pdb_id: 5OND
    chain_id: A
    # VERIFY: check deposited residue range from RCSB before structure cleaning
    residue_range: 1..162 (verify)
    has_mutations: false
    notes: >
      Free/NusG-like (autoinhibited) state with CTD in beta-barrel fold.
      PDB 5OND is proposed to contain the full-length autoinhibited RfaH
      with NTD in ops element-bound form. Chain ID and deposited residue
      range MUST be confirmed against RCSB before structure cleaning.
    qc:
      # VERIFY: fill in method, resolution, chains from RCSB HEADER
      method: x-ray (verify)
      resolution_A: null
      n_models: null
      chains_all: []
      chain_used: A
      chains_dropped: []
      missing_residues: []
      mutations_vs_canonical: []
      b_factor_mean: null
      heteroatoms_removed: []
  - name: state_B_fold_switched
    # VERIFY: 6C6S is proposed fold-switched form; alternatively consider
    # 2LCL (isolated CTD beta-barrel, NMR) or 2LCO (isolated CTD alpha, NMR)
    # for the CTD-only structures. All IDs must be checked against RCSB.
    pdb_id: 6C6S
    chain_id: A
    # VERIFY: 6C6S may be a full-length NTD-CTD structure; confirm residue range
    residue_range: 1..162 (verify)
    has_mutations: false
    notes: >
      Fold-switched state with CTD in alpha-helical hairpin conformation.
      If a full-length fold-switched structure is unavailable, consider using
      the isolated CTD structures (e.g. 2LCO for alpha-helical CTD, NMR).
      PDB ID, chain, method, and residue range MUST be verified against RCSB
      before structure cleaning and renumbering.
    qc:
      # VERIFY: fill in method, resolution, chains from RCSB HEADER
      method: x-ray or NMR (verify)
      resolution_A: null
      n_models: null
      chains_all: []
      chain_used: A
      chains_dropped: []
      missing_residues: []
      mutations_vs_canonical: []
      b_factor_mean: null
      heteroatoms_removed: []
- case_name: MAD2
  tier: 1
  classification: known-state
  query_source_db: UniProt
  query_accession: O43684
  query_organism: Homo sapiens
  # VERIFY: fetch canonical sequence from UniProt O43684 before AF2 runs
  canonical_query_sequence: SEE_UNIPROT_O43684
  canonical_query_length: 205
  canonical_query_frame: UniProt 1..205 (full-length MAD2L1)
  construct_start: 1
  construct_end: 205
  biology: >
    MAD2 (MAD2L1) is a spindle assembly checkpoint protein that exists in two
    conformational states: open (O-MAD2, N1 fold) and closed (C-MAD2, N2 fold).
    The switch involves massive topological rearrangement of the C-terminal
    "safety belt" region. Closed MAD2 is the active form that sequesters CDC20
    to inhibit APC/C. Approximately 205 aa (human MAD2L1).
  states:
  - name: state_A_open_O_MAD2
    # VERIFY: confirm 1DUJ chain A is monomeric open-state MAD2 from RCSB
    pdb_id: 1DUJ
    chain_id: A
    # VERIFY: crystal may be missing terminal residues; confirm exact range from RCSB
    residue_range: 1..196 (verify)
    has_mutations: false
    notes: >
      Open state (O-MAD2, N1 fold) monomer. The C-terminal safety belt is in
      open topology. Deposited residue range may not cover all 205 residues;
      verify from RCSB SEQRES/ATOM records before cleaning.
    qc:
      # VERIFY: fill in method, resolution, chains from RCSB HEADER
      method: x-ray diffraction (verify)
      resolution_A: null
      n_models: null
      chains_all: []
      chain_used: A
      chains_dropped: []
      missing_residues: []
      mutations_vs_canonical: []
      b_factor_mean: null
      heteroatoms_removed: []
  - name: state_B_closed_C_MAD2
    # VERIFY: 2V64 contains CDC20 peptide; if ligand-free closed state is
    # preferred, check 1KLQ or other deposits. Confirm chain ID from RCSB.
    pdb_id: 2V64
    chain_id: A
    # VERIFY: crystal may be missing terminal residues; confirm from RCSB
    residue_range: 1..196 (verify)
    has_mutations: false
    notes: >
      Closed state (C-MAD2, N2 fold) with CDC20 peptide bound; the safety belt
      wraps around the ligand in a different topology from the open state.
      If a ligand-free closed-state structure is available (e.g. 1KLQ), prefer
      it. Chain ID and residue range MUST be verified against RCSB before
      structure cleaning.
    qc:
      # VERIFY: fill in method, resolution, chains from RCSB HEADER
      method: x-ray diffraction (verify)
      resolution_A: null
      n_models: null
      chains_all: []
      chain_used: A
      chains_dropped: []
      missing_residues: []
      mutations_vs_canonical: []
      b_factor_mean: null
      heteroatoms_removed: []
generated_at: '2026-04-22T18:42:00Z'
updated_at: '2026-04-24T00:00:00Z'