SMTL ID : 5z68.2 (1 other biounit)

Structure of the recombination mediator protein RecF-ATP in RecFOR pathway

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 22 residues within 4Å: Chain A: R.20, N.21, N.40, A.41, Q.42, G.43, K.44, S.45, N.46, R.61, E.67, V.69, K.70, F.71, D.324 Chain B: Y.289, S.290, S.291, Q.292, G.293, Q.294 Ligands: MG.6 22 PLIP interactions: 16 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:R.20, A:A.41, A:A.41, A:Q.42, A:G.43, A:K.44, A:S.45, A:N.46, A:N.46, A:V.69, A:F.71, A:D.324, B:S.291, B:Q.292, B:G.293, B:Q.294 Salt bridges: A:K.44, A:K.44, A:R.61 pi-Stacking: A:F.71 Water bridges: B:Q.294, B:Q.294 ATP.7: 21 residues within 4Å: Chain A: Y.289, S.291, Q.292, G.293, Q.294 Chain B: R.20, N.21, L.39, N.40, Q.42, G.43, K.44, S.45, N.46, R.61, E.67, V.69, K.70, F.71, D.324 Ligands: MG.14 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.20, B:N.21, B:N.40, B:G.43, B:K.44, B:S.45, B:N.46, B:N.46, B:V.69, B:F.71, A:S.291, A:Q.292, A:G.293 Salt bridges: B:K.44, B:R.61 pi-Stacking: B:F.71

10 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 6 residues within 4Å: Chain A: R.52, M.56, R.58, S.59, F.60, A.147 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.52, A:R.58 IMD.3: 3 residues within 4Å: Chain A: K.23, K.24, K.70 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.24, A:K.70 pi-Cation interactions: A:K.70 IMD.4: 3 residues within 4Å: Chain A: G.137, P.138, S.139 No protein-ligand interaction detected (PLIP) IMD.5: 1 residues within 4Å: Chain A: L.307 No protein-ligand interaction detected (PLIP) IMD.8: 4 residues within 4Å: Chain B: R.52, M.56, R.58, F.60 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.52, B:R.58 IMD.9: 1 residues within 4Å: Chain B: T.114 No protein-ligand interaction detected (PLIP) IMD.10: 2 residues within 4Å: Chain B: K.64, M.65 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.65 IMD.11: 4 residues within 4Å: Chain B: G.137, P.138, S.139 Ligands: IMD.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.139 IMD.12: 4 residues within 4Å: Chain B: P.138, R.142, R.274 Ligands: IMD.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.142 IMD.13: 2 residues within 4Å: Chain B: L.307, K.340 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain A: S.45, R.61 Ligands: ATP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.45, H2O.1, H2O.1 MG.14: 3 residues within 4Å: Chain A: Q.292 Chain B: S.45 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tang, Q. et al., ATP-dependent conformational change in ABC-ATPase RecF serves as a switch in DNA repair. Sci Rep (2018)

Release Date

2018-04-18

Peptides

DNA replication and repair protein RecF: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

DNA replication and repair protein RecF

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