SMTL ID : 8a3v.1

Crystal structure of the Vibrio cholerae replicative helicase (VcDnaB) in complex with its loader protein (VcDciA)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-6-6-mer

Ligands

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

ADP.1: 21 residues within 4Å: Chain A: R.229, P.230, S.231, M.232, G.233, K.234, T.235, T.236, M.260, R.268, Q.278, T.279, Y.341, R.417, F.450, G.452, H.453 Chain B: G.441, P.442, I.443 Ligands: MG.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:R.229, A:S.231, A:S.231, A:M.232, A:G.233, A:K.234, A:T.235, A:T.235, A:T.236, A:T.236, A:T.279, A:T.279, A:T.279, A:Y.341, A:R.417 Salt bridges: A:K.234, A:R.268 ADP.3: 18 residues within 4Å: Chain B: R.229, P.230, S.231, M.232, G.233, K.234, T.235, T.236, M.260, R.268, Q.278, T.279, Y.341, R.417, F.450, G.452, H.453 Ligands: MG.4 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:R.229, B:S.231, B:S.231, B:M.232, B:G.233, B:K.234, B:T.235, B:T.235, B:T.236, B:T.236, B:T.279, B:T.279, B:T.279, B:Y.341, B:R.417 Salt bridges: B:K.234, B:R.268 ADP.5: 21 residues within 4Å: Chain D: R.229, P.230, S.231, M.232, G.233, K.234, T.235, T.236, M.260, R.268, Q.278, T.279, Y.341, R.417, F.450, G.452, H.453 Chain E: G.441, P.442, I.443 Ligands: MG.6 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:R.229, D:S.231, D:S.231, D:M.232, D:G.233, D:K.234, D:T.235, D:T.235, D:T.236, D:T.236, D:T.279, D:T.279, D:T.279, D:Y.341, D:R.417 Salt bridges: D:K.234, D:R.268 ADP.7: 18 residues within 4Å: Chain E: R.229, P.230, S.231, M.232, G.233, K.234, T.235, T.236, M.260, R.268, Q.278, T.279, Y.341, R.417, F.450, G.452, H.453 Ligands: MG.8 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:R.229, E:S.231, E:S.231, E:M.232, E:G.233, E:K.234, E:T.235, E:T.235, E:T.236, E:T.236, E:T.279, E:T.279, E:T.279, E:Y.341, E:R.417 Salt bridges: E:K.234, E:R.268 ADP.9: 21 residues within 4Å: Chain G: R.229, P.230, S.231, M.232, G.233, K.234, T.235, T.236, M.260, R.268, Q.278, T.279, Y.341, R.417, F.450, G.452, H.453 Chain H: G.441, P.442, I.443 Ligands: MG.10 17 PLIP interactions: 17 interactions with chain G Hydrogen bonds: G:R.229, G:S.231, G:S.231, G:M.232, G:G.233, G:K.234, G:T.235, G:T.235, G:T.236, G:T.236, G:T.279, G:T.279, G:T.279, G:Y.341, G:R.417 Salt bridges: G:K.234, G:R.268 ADP.11: 18 residues within 4Å: Chain H: R.229, P.230, S.231, M.232, G.233, K.234, T.235, T.236, M.260, R.268, Q.278, T.279, Y.341, R.417, F.450, G.452, H.453 Ligands: MG.12 17 PLIP interactions: 17 interactions with chain H Hydrogen bonds: H:R.229, H:S.231, H:S.231, H:M.232, H:G.233, H:K.234, H:T.235, H:T.235, H:T.236, H:T.236, H:T.279, H:T.279, H:T.279, H:Y.341, H:R.417 Salt bridges: H:K.234, H:R.268

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: T.235, E.259, M.260, D.340, Y.341 Ligands: ADP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.235, A:D.340 MG.4: 6 residues within 4Å: Chain B: T.235, E.259, M.260, D.340, Y.341 Ligands: ADP.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.235, B:D.340 MG.6: 6 residues within 4Å: Chain D: T.235, E.259, M.260, D.340, Y.341 Ligands: ADP.5 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.235, D:D.340 MG.8: 6 residues within 4Å: Chain E: T.235, E.259, M.260, D.340, Y.341 Ligands: ADP.7 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.235, E:D.340 MG.10: 6 residues within 4Å: Chain G: T.235, E.259, M.260, D.340, Y.341 Ligands: ADP.9 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:T.235, G:D.340 MG.12: 6 residues within 4Å: Chain H: T.235, E.259, M.260, D.340, Y.341 Ligands: ADP.11 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:T.235, H:D.340

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cargemel, C. et al., The LH-DH module of bacterial replicative helicases is the common binding site for DciA and other helicase loaders. Acta Crystallogr D Struct Biol (2023)

Release Date

2023-02-15

Peptides

Replicative DNA helicase: ABDEGH
DUF721 domain-containing protein: CFIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
A

E
B

G
A

H
B

C
C

F
C

I
C

J
D

K
D

L
D

Replicative DNA helicase

DUF721 domain-containing protein

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