SMTL ID : 7jy7.1

Structure of a 12 base pair RecA-D loop complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 2.90 Å

Oligo State

homo-9-mer

Ligands

9 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.74, E.97, D.145 Ligands: AGS.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.74 MG.3: 5 residues within 4Å: Chain A: K.251 Chain B: T.74, E.97, D.145 Ligands: AGS.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.74 MG.5: 5 residues within 4Å: Chain B: K.251 Chain C: T.74, E.97, D.145 Ligands: AGS.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.74 MG.7: 5 residues within 4Å: Chain C: K.251 Chain D: T.74, E.97, D.145 Ligands: AGS.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.74 MG.9: 5 residues within 4Å: Chain D: K.251 Chain E: T.74, E.97, D.145 Ligands: AGS.10 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.74 MG.11: 6 residues within 4Å: Chain F: K.73, T.74, E.97, D.145, I.193 Ligands: AGS.12 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.74 MG.13: 4 residues within 4Å: Chain G: T.74, E.97, D.145 Ligands: AGS.14 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.74 MG.15: 4 residues within 4Å: Chain H: T.74, E.97, D.145 Ligands: AGS.16 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:T.74 MG.17: 4 residues within 4Å: Chain I: T.74, E.97, D.145 Ligands: AGS.18 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:T.74

9 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.2: 16 residues within 4Å: Chain A: E.69, S.70, S.71, G.72, K.73, T.74, T.75, E.97, D.101, Y.104, S.146, Q.195, S.241, I.263, Y.265 Ligands: MG.1 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.70, A:S.71, A:G.72, A:K.73, A:T.74, A:T.74, A:T.75, A:T.75, A:D.101, A:Y.104 Salt bridges: A:K.73 pi-Stacking: A:Y.104, A:Y.104 AGS.4: 24 residues within 4Å: Chain A: F.218, K.249, N.250, K.251, I.252, A.253, A.254, P.255, F.256 Chain B: E.69, S.70, S.71, G.72, K.73, T.74, T.75, E.97, D.101, Y.104, Q.195, S.241, I.263, Y.265 Ligands: MG.3 15 PLIP interactions: 4 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:F.218, A:K.249, A:K.251, A:K.251, B:S.70, B:S.71, B:G.72, B:K.73, B:T.74, B:T.75, B:Y.104, B:S.241 Salt bridges: B:K.73 pi-Stacking: B:Y.104, B:Y.104 AGS.6: 23 residues within 4Å: Chain B: F.218, K.249, N.250, K.251, I.252, A.253, A.254, P.255, F.256 Chain C: E.69, S.70, S.71, G.72, K.73, T.74, T.75, E.97, D.101, Y.104, S.241, I.263, Y.265 Ligands: MG.5 18 PLIP interactions: 15 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:S.70, C:S.71, C:G.72, C:K.73, C:T.74, C:T.74, C:T.75, C:T.75, C:E.97, C:D.101, C:Y.104, C:S.241, B:F.218, B:K.249, B:K.251 Salt bridges: C:K.73 pi-Stacking: C:Y.104, C:Y.104 AGS.8: 24 residues within 4Å: Chain C: F.218, K.249, N.250, K.251, I.252, A.253, A.254, P.255, F.256 Chain D: E.69, S.70, S.71, G.72, K.73, T.74, T.75, E.97, D.101, Y.104, S.241, I.263, Y.265, G.266 Ligands: MG.7 16 PLIP interactions: 14 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.70, D:S.71, D:G.72, D:K.73, D:T.74, D:T.74, D:T.75, D:T.75, D:D.101, D:Y.104, D:S.241, C:K.249, C:K.251 Salt bridges: D:K.73 pi-Stacking: D:Y.104, D:Y.104 AGS.10: 24 residues within 4Å: Chain D: F.218, K.249, N.250, K.251, I.252, A.253, A.254, P.255, F.256 Chain E: E.69, S.70, S.71, G.72, K.73, T.74, T.75, E.97, D.101, Y.104, S.241, I.263, Y.265, G.266 Ligands: MG.9 17 PLIP interactions: 14 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:S.70, E:S.71, E:G.72, E:K.73, E:T.74, E:T.74, E:T.75, E:T.75, E:E.97, E:Y.104, E:S.241, D:K.249, D:K.251, D:K.251 Salt bridges: E:K.73 pi-Stacking: E:Y.104, E:Y.104 AGS.12: 24 residues within 4Å: Chain E: F.218, K.249, N.250, K.251, I.252, A.253, A.254, P.255, F.256 Chain F: E.69, S.70, S.71, G.72, K.73, T.74, T.75, E.97, D.101, Y.104, S.241, I.263, Y.265, G.266 Ligands: MG.11 19 PLIP interactions: 15 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:S.70, F:S.70, F:S.70, F:S.71, F:G.72, F:K.73, F:T.74, F:T.75, F:T.75, F:E.97, F:Y.104, F:S.241, E:K.249, E:N.250, E:K.251, E:K.251 Salt bridges: F:K.73 pi-Stacking: F:Y.104, F:Y.104 AGS.14: 24 residues within 4Å: Chain F: F.218, K.249, N.250, K.251, I.252, A.253, A.254, P.255, F.256 Chain G: E.69, S.70, S.71, G.72, K.73, T.74, T.75, E.97, D.101, Y.104, S.241, I.263, Y.265, G.266 Ligands: MG.13 15 PLIP interactions: 11 interactions with chain G, 4 interactions with chain F Hydrogen bonds: G:S.70, G:S.71, G:G.72, G:K.73, G:T.74, G:T.75, G:T.75, G:Y.104, F:F.218, F:K.249, F:K.251, F:K.251 Salt bridges: G:K.73 pi-Stacking: G:Y.104, G:Y.104 AGS.16: 23 residues within 4Å: Chain G: F.218, K.249, N.250, K.251, I.252, A.253, A.254, P.255, F.256 Chain H: E.69, S.70, S.71, G.72, K.73, T.74, T.75, E.97, D.101, Y.104, S.241, I.263, Y.265 Ligands: MG.15 17 PLIP interactions: 3 interactions with chain G, 14 interactions with chain H Hydrogen bonds: G:F.218, G:K.249, G:K.251, H:S.70, H:S.71, H:G.72, H:K.73, H:T.74, H:T.74, H:T.75, H:T.75, H:D.101, H:Y.104, H:S.241 Salt bridges: H:K.73 pi-Stacking: H:Y.104, H:Y.104 AGS.18: 25 residues within 4Å: Chain H: F.218, K.249, N.250, K.251, I.252, A.253, A.254, P.255, F.256 Chain I: E.69, S.70, S.71, G.72, K.73, T.74, T.75, E.97, D.101, Y.104, Q.195, S.241, I.263, Y.265, G.266 Ligands: MG.17 15 PLIP interactions: 11 interactions with chain I, 4 interactions with chain H Hydrogen bonds: I:S.70, I:S.71, I:G.72, I:K.73, I:T.74, I:T.75, I:T.75, I:Y.104, H:F.218, H:K.249, H:K.251, H:K.251 Salt bridges: I:K.73 pi-Stacking: I:Y.104, I:Y.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, H. et al., Mechanism of strand exchange from RecA-DNA synaptic and D-loop structures. Nature (2020)

Release Date

2020-11-04

Peptides

Protein RecA: ABCDEFGHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

Protein RecA

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