SMTL ID : 8aaj.1

Crystal structure of the Pyrococcus abyssi RPA (apo form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.70 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.218, C.221, C.236, H.239 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.218, A:C.221, A:C.236, A:H.239

11 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: R.116, S.147, S.149, L.151 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.147, A:S.149 Salt bridges: A:R.116, A:K.223 SO4.3: 4 residues within 4Å: Chain A: Y.210, R.211, R.262, R.300 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.211, A:R.262, A:R.300 SO4.4: 4 residues within 4Å: Chain A: R.211, K.296, F.326, L.327 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.211, A:K.296 SO4.5: 2 residues within 4Å: Chain A: K.191, D.192 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.191 SO4.6: 2 residues within 4Å: Chain A: R.187, R.347 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.187 Salt bridges: A:R.347 SO4.7: 2 residues within 4Å: Chain A: T.184, R.318 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.318 SO4.8: 4 residues within 4Å: Chain A: G.113, R.114, R.198, F.199 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.114 Salt bridges: A:R.114, A:R.198 SO4.9: 3 residues within 4Å: Chain B: R.52, E.53, K.91 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.53 Salt bridges: B:R.52, B:K.91 SO4.10: 5 residues within 4Å: Chain A: K.208 Chain B: R.5, R.43, K.100, E.113 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:K.208, B:R.5, B:K.100 Hydrogen bonds: B:R.43 SO4.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.12: 5 residues within 4Å: Chain B: Q.66, W.75 Chain C: R.11, R.12, R.13 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Q.66, B:W.75, C:R.13 Salt bridges: C:R.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Madru, C. et al., DNA-binding mechanism and evolution of replication protein A. Nat Commun (2023)

Release Date

2023-05-03

Peptides

Replication factor A: A
RPA32 subunit of the hetero-oligomeric complex involved in homologous recombination: B
RPA14 subunit of the hetero-oligomeric complex involved in homologous recombination: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Replication factor A

RPA32 subunit of the hetero-oligomeric complex involved in homologous recombination

RPA14 subunit of the hetero-oligomeric complex involved in homologous recombination

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