SMTL ID : 8gj0.1

E. coli clamp loader with open clamp on primed template DNA (form 1)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ADP.1: 23 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, L.178, Q.186, L.214, R.215, L.218 Chain C: E.144 Ligands: MG.2, ALF.3 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:W.10, B:W.10, B:R.11, B:V.19, B:G.48, B:V.49, B:V.49, B:G.50, B:K.51, B:T.52, B:T.52 Salt bridges: B:R.11, B:K.51, B:R.215 ADP.5: 25 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, L.178, Q.186, L.214, R.215, L.218 Chain D: E.144, R.169 Ligands: MG.6, ALF.8 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:A.7, C:V.19, C:T.46, C:G.48, C:V.49, C:V.49, C:G.50, C:K.51, C:T.52, C:T.52, C:S.53, C:S.53 Salt bridges: C:R.11, C:K.51, C:R.215, C:R.215 ADP.9: 22 residues within 4Å: Chain D: L.6, 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, L.178, L.214, R.215, L.218 Ligands: MG.10, ALF.11 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:W.10, D:V.19, D:V.19, D:G.48, D:V.49, D:G.50, D:K.51, D:T.52, D:T.52, D:S.53, D:S.53 Salt bridges: D:R.11, D:K.51, D:R.215, D:R.215

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain B: T.52, D.126 Chain C: E.144 Ligands: ADP.1, ALF.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.52 MG.6: 5 residues within 4Å: Chain C: T.52, D.126 Chain D: R.169 Ligands: ADP.5, ALF.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.52 MG.10: 6 residues within 4Å: Chain D: T.52, D.126, R.215 Chain E: E.133 Ligands: ADP.9, ALF.11 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.52

3 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.3: 11 residues within 4Å: Chain B: R.47, G.48, K.51, T.52, T.157, R.215 Chain C: E.144, T.165, R.169 Ligands: ADP.1, MG.2 No protein-ligand interaction detected (PLIP) ALF.8: 12 residues within 4Å: Chain C: T.46, R.47, G.48, K.51, T.52, T.157, R.215 Chain D: E.144, T.165, R.169 Ligands: ADP.5, MG.6 No protein-ligand interaction detected (PLIP) ALF.11: 12 residues within 4Å: Chain D: R.47, G.48, K.51, T.52, E.127, T.157, R.215 Chain E: E.133, T.154, R.158 Ligands: ADP.9, MG.10 No protein-ligand interaction detected (PLIP)

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 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.7: 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.12: 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.13: 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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