SMTL ID : 8giy.1

E. coli clamp loader with closed clamp

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-3-1-1-2-mer

Ligands

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

AGS.1: 22 residues within 4Å: Chain B: A.7, W.10, R.11, P.12, D.17, V.18, V.19, Q.21, R.47, G.48, V.49, G.50, K.51, T.52, S.53, T.157, L.178, Q.186, L.214, R.215, L.218 Ligands: MG.2 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:A.7, B:A.7, B:V.19, B:G.48, B:V.49, B:V.49, B:G.50, B:K.51, B:K.51, B:T.52, B:T.52, B:S.53, B:S.53, B:R.215, B:R.215 Salt bridges: B:R.11, B:K.51, B:R.215, B:R.215 AGS.4: 23 residues within 4Å: Chain C: A.7, R.8, W.10, R.11, P.12, D.17, V.18, V.19, Q.21, R.47, G.48, V.49, G.50, K.51, T.52, S.53, T.157, L.178, Q.186, L.214, R.215, L.218 Ligands: MG.5 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:A.7, C:A.7, C:V.19, C:G.48, C:V.49, C:V.49, C:G.50, C:K.51, C:K.51, C:T.52, C:E.127, C:T.157, C:R.215 Salt bridges: C:R.11, C:K.51, C:R.215, C:R.215 AGS.7: 25 residues within 4Å: Chain D: A.7, W.10, R.11, P.12, D.17, V.18, V.19, Q.21, T.46, R.47, G.48, V.49, G.50, K.51, T.52, S.53, T.157, L.178, L.214, R.215, L.218 Chain E: E.133, T.154, R.158 Ligands: MG.8 18 PLIP interactions: 17 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:A.7, D:V.19, D:G.48, D:V.49, D:V.49, D:G.50, D:K.51, D:K.51, D:T.52, D:T.52, D:S.53, D:S.53, D:R.215, E:R.158 Salt bridges: D:R.11, D:K.51, D:R.215, D:R.215

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain B: T.52 Ligands: AGS.1 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.52 MG.5: 2 residues within 4Å: Chain C: T.52 Ligands: AGS.4 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.52 MG.8: 4 residues within 4Å: Chain D: T.52, D.126, R.215 Ligands: AGS.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.52

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 7 residues within 4Å: Chain B: C.64, E.65, C.73, G.74, V.75, C.76, C.79 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.64, B:C.73, B:C.76, B:C.79 ZN.6: 7 residues within 4Å: Chain C: C.64, E.65, C.73, G.74, V.75, C.76, C.79 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.64, C:C.73, C:C.76, C:C.79 ZN.9: 7 residues within 4Å: Chain D: C.64, E.65, C.73, G.74, V.75, C.76, C.79 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.64, D:C.73, D:C.76, D:C.79 ZN.10: 9 residues within 4Å: Chain E: C.50, Q.51, Q.52, S.58, C.59, G.60, H.61, C.62, C.65 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.50, E:C.59, E:C.62, E:C.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Z.Q. et al., Structural characterisation of the complete cycle of sliding clamp loading in Escherichia coli. Nat Commun (2024)

Release Date

2024-03-27

Peptides

DNA polymerase III subunit delta: A
DNA polymerase III subunit tau: BCD
DNA polymerase III subunit delta': E
DNA polymerase III subunit psi: F
Beta sliding clamp: GH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
H

H
I

DNA polymerase III subunit delta

DNA polymerase III subunit tau

DNA polymerase III subunit delta'

DNA polymerase III subunit psi

Beta sliding clamp

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