SMTL ID : 5jrj.1

Crystal Structure of Herbaspirillum seropedicae RecA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-hexamer

Ligands

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 16 residues within 4Å: Chain A: P.74, E.75, S.76, S.77, G.78, K.79, T.80, T.81, D.107, Y.110, K.113, I.269, L.270, Y.271, G.272 Ligands: ATP.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:P.74, A:S.76, A:S.77, A:G.78, A:K.79, A:T.80, A:T.81, A:T.81, A:D.107, A:G.272 Water bridges: A:E.75, A:E.75, A:K.79, A:T.80, A:K.113, A:Y.271 Salt bridges: A:K.79 pi-Stacking: A:Y.110, A:Y.110, A:Y.271 ADP.4: 16 residues within 4Å: Chain B: P.74, E.75, S.76, S.77, G.78, K.79, T.80, T.81, D.107, Y.110, K.113, I.269, L.270, Y.271, G.272 Ligands: ATP.5 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:P.74, B:S.76, B:S.77, B:G.78, B:K.79, B:T.80, B:T.81, B:T.81, B:D.107, B:G.272 Water bridges: B:E.75, B:E.75, B:K.79, B:T.80, B:K.113, B:Y.271 Salt bridges: B:K.79 pi-Stacking: B:Y.110, B:Y.110, B:Y.271 ADP.7: 16 residues within 4Å: Chain C: P.74, E.75, S.76, S.77, G.78, K.79, T.80, T.81, D.107, Y.110, K.113, I.269, L.270, Y.271, G.272 Ligands: ATP.8 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:P.74, C:S.76, C:S.77, C:G.78, C:K.79, C:T.80, C:T.81, C:T.81, C:D.107, C:G.272 Water bridges: C:E.75, C:E.75, C:K.79, C:T.80, C:K.113, C:Y.271 Salt bridges: C:K.79 pi-Stacking: C:Y.110, C:Y.110, C:Y.271 ADP.10: 16 residues within 4Å: Chain D: P.74, E.75, S.76, S.77, G.78, K.79, T.80, T.81, D.107, Y.110, K.113, I.269, L.270, Y.271, G.272 Ligands: ATP.11 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:P.74, D:S.76, D:S.77, D:G.78, D:K.79, D:T.80, D:T.81, D:T.81, D:D.107, D:G.272 Water bridges: D:E.75, D:E.75, D:K.79, D:T.80, D:K.113, D:Y.271 Salt bridges: D:K.79 pi-Stacking: D:Y.110, D:Y.110, D:Y.271 ADP.13: 16 residues within 4Å: Chain E: P.74, E.75, S.76, S.77, G.78, K.79, T.80, T.81, D.107, Y.110, K.113, I.269, L.270, Y.271, G.272 Ligands: ATP.14 20 PLIP interactions: 20 interactions with chain E Hydrogen bonds: E:P.74, E:S.76, E:S.77, E:G.78, E:K.79, E:T.80, E:T.81, E:T.81, E:D.107, E:G.272 Water bridges: E:E.75, E:E.75, E:K.79, E:T.80, E:K.113, E:Y.271 Salt bridges: E:K.79 pi-Stacking: E:Y.110, E:Y.110, E:Y.271 ADP.16: 16 residues within 4Å: Chain F: P.74, E.75, S.76, S.77, G.78, K.79, T.80, T.81, D.107, Y.110, K.113, I.269, L.270, Y.271, G.272 Ligands: ATP.17 20 PLIP interactions: 20 interactions with chain F Hydrogen bonds: F:P.74, F:S.76, F:S.77, F:G.78, F:K.79, F:T.80, F:T.81, F:T.81, F:D.107, F:G.272 Water bridges: F:E.75, F:E.75, F:K.79, F:T.80, F:K.113, F:Y.271 Salt bridges: F:K.79 pi-Stacking: F:Y.110, F:Y.110, F:Y.271

6 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Covalent)

ATP.2: 16 residues within 4Å: Chain A: P.74, E.75, S.76, S.77, G.78, K.79, T.80, T.81, D.107, Y.110, K.113, Q.201, I.269, Y.271, G.272 Ligands: ADP.1 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:E.75, A:E.75, A:S.76, A:S.77, A:G.78, A:K.79, A:T.80, A:T.81, A:T.81, A:D.107, A:Q.201, A:G.272 Water bridges: A:E.75, A:E.75, A:E.75, A:K.79, A:K.79, A:T.80, A:T.80, A:T.80, A:T.109, A:K.113 Salt bridges: A:K.79, A:K.79 pi-Stacking: A:Y.110, A:Y.110, A:Y.271 ATP.5: 16 residues within 4Å: Chain B: P.74, E.75, S.76, S.77, G.78, K.79, T.80, T.81, D.107, Y.110, K.113, Q.201, I.269, Y.271, G.272 Ligands: ADP.4 27 PLIP interactions: 27 interactions with chain B Hydrogen bonds: B:E.75, B:E.75, B:S.76, B:S.77, B:G.78, B:K.79, B:T.80, B:T.81, B:T.81, B:D.107, B:Q.201, B:G.272 Water bridges: B:E.75, B:E.75, B:E.75, B:K.79, B:K.79, B:T.80, B:T.80, B:T.80, B:T.109, B:K.113 Salt bridges: B:K.79, B:K.79 pi-Stacking: B:Y.110, B:Y.110, B:Y.271 ATP.8: 16 residues within 4Å: Chain C: P.74, E.75, S.76, S.77, G.78, K.79, T.80, T.81, D.107, Y.110, K.113, Q.201, I.269, Y.271, G.272 Ligands: ADP.7 27 PLIP interactions: 27 interactions with chain C Hydrogen bonds: C:E.75, C:E.75, C:S.76, C:S.77, C:G.78, C:K.79, C:T.80, C:T.81, C:T.81, C:D.107, C:Q.201, C:G.272 Water bridges: C:E.75, C:E.75, C:E.75, C:K.79, C:K.79, C:T.80, C:T.80, C:T.80, C:T.109, C:K.113 Salt bridges: C:K.79, C:K.79 pi-Stacking: C:Y.110, C:Y.110, C:Y.271 ATP.11: 16 residues within 4Å: Chain D: P.74, E.75, S.76, S.77, G.78, K.79, T.80, T.81, D.107, Y.110, K.113, Q.201, I.269, Y.271, G.272 Ligands: ADP.10 27 PLIP interactions: 27 interactions with chain D Hydrogen bonds: D:E.75, D:E.75, D:S.76, D:S.77, D:G.78, D:K.79, D:T.80, D:T.81, D:T.81, D:D.107, D:Q.201, D:G.272 Water bridges: D:E.75, D:E.75, D:E.75, D:K.79, D:K.79, D:T.80, D:T.80, D:T.80, D:T.109, D:K.113 Salt bridges: D:K.79, D:K.79 pi-Stacking: D:Y.110, D:Y.110, D:Y.271 ATP.14: 16 residues within 4Å: Chain E: P.74, E.75, S.76, S.77, G.78, K.79, T.80, T.81, D.107, Y.110, K.113, Q.201, I.269, Y.271, G.272 Ligands: ADP.13 27 PLIP interactions: 27 interactions with chain E Hydrogen bonds: E:E.75, E:E.75, E:S.76, E:S.77, E:G.78, E:K.79, E:T.80, E:T.81, E:T.81, E:D.107, E:Q.201, E:G.272 Water bridges: E:E.75, E:E.75, E:E.75, E:K.79, E:K.79, E:T.80, E:T.80, E:T.80, E:T.109, E:K.113 Salt bridges: E:K.79, E:K.79 pi-Stacking: E:Y.110, E:Y.110, E:Y.271 ATP.17: 16 residues within 4Å: Chain F: P.74, E.75, S.76, S.77, G.78, K.79, T.80, T.81, D.107, Y.110, K.113, Q.201, I.269, Y.271, G.272 Ligands: ADP.16 27 PLIP interactions: 27 interactions with chain F Hydrogen bonds: F:E.75, F:E.75, F:S.76, F:S.77, F:G.78, F:K.79, F:T.80, F:T.81, F:T.81, F:D.107, F:Q.201, F:G.272 Water bridges: F:E.75, F:E.75, F:E.75, F:K.79, F:K.79, F:T.80, F:T.80, F:T.80, F:T.109, F:K.113 Salt bridges: F:K.79, F:K.79 pi-Stacking: F:Y.110, F:Y.110, F:Y.271

6 x CA: CALCIUM ION(Non-covalent)

CA.3: 2 residues within 4Å: Chain A: N.119, D.120 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.120, H2O.10, H2O.10, H2O.64, H2O.73 CA.6: 2 residues within 4Å: Chain B: N.119, D.120 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.120, H2O.22, H2O.23, H2O.39, H2O.48 CA.9: 2 residues within 4Å: Chain C: N.119, D.120 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.120, H2O.35, H2O.35, H2O.52, H2O.60 CA.12: 2 residues within 4Å: Chain D: N.119, D.120 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.120, H2O.27, H2O.35, H2O.47, H2O.48 CA.15: 2 residues within 4Å: Chain E: N.119, D.120 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.120, H2O.54, H2O.60, H2O.60 CA.18: 2 residues within 4Å: Chain F: N.119, D.120 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:D.120, H2O.14, H2O.23, H2O.72, H2O.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leite, W.C. et al., Structural and Functional Studies of H. seropedicae RecA Protein - Insights into the Polymerization of RecA Protein as Nucleoprotein Filament. PLoS ONE (2016)

Release Date

2016-08-03

Peptides

Protein RecA: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Protein RecA