SMTL ID : 8uh7.1

Structure of T4 Bacteriophage clamp loader bound to the T4 clamp, primer-template DNA, and ATP analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.63 Å

Oligo State

hetero-1-4-3-mer

Ligands

3 x 08T: [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium(Non-covalent)

08T.1: 23 residues within 4Å: Chain B: E.17, Y.20, R.21, P.22, C.28, I.29, L.30, P.57, G.58, T.59, G.60, K.61, T.62, T.63, E.113, N.144, R.180, F.209, R.210, I.213 Chain C: E.131, R.156 Ligands: MG.2 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:Y.20, B:R.21, B:I.29, B:G.58, B:T.59, B:T.59, B:T.59, B:G.60, B:K.61, B:T.62, B:T.62, B:T.63, B:T.63 Salt bridges: B:R.21, B:K.61, B:R.210, B:R.210 pi-Stacking: B:F.209, B:F.209 08T.3: 20 residues within 4Å: Chain C: E.17, Y.20, R.21, P.22, I.29, P.57, G.58, T.59, G.60, K.61, T.62, T.63, E.113, N.144, F.209, R.210, I.213 Chain D: E.131, R.156 Ligands: MG.4 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:Y.20, C:R.21, C:I.29, C:G.58, C:T.59, C:T.59, C:G.60, C:K.61, C:T.62, C:T.63, C:T.63 Water bridges: C:R.180 Salt bridges: C:R.21, C:K.61, C:R.210, C:R.210 pi-Stacking: C:F.209 08T.5: 21 residues within 4Å: Chain D: E.17, Y.20, R.21, P.22, C.28, I.29, P.57, G.58, T.59, G.60, K.61, T.62, T.63, E.113, N.144, F.209, R.210, I.213 Chain E: E.131, R.156 Ligands: MG.6 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:Y.20, D:R.21, D:I.29, D:G.58, D:T.59, D:T.59, D:G.60, D:K.61, D:T.62, D:T.62, D:T.63, D:T.63 Water bridges: D:K.61 Salt bridges: D:R.21, D:K.61, D:R.210, D:R.210

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain B: T.62, D.112, E.113 Chain C: E.131, R.156 Ligands: 08T.1 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.62, B:E.113 MG.4: 6 residues within 4Å: Chain C: T.62, D.112, E.113 Chain D: E.131, R.156 Ligands: 08T.3 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.62, C:E.113 MG.6: 6 residues within 4Å: Chain D: T.62, D.112, E.113 Chain E: E.131, R.156 Ligands: 08T.5 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.62, D:E.113 MG.8: 5 residues within 4Å: Chain E: K.61, T.62, D.112, E.113 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.62

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

ADP.7: 17 residues within 4Å: Chain E: E.17, Y.20, R.21, P.22, C.28, I.29, L.30, G.58, T.59, G.60, K.61, T.62, T.63, F.209, R.210, I.213 Ligands: MG.8 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:E.17, E:Y.20, E:I.29, E:G.58, E:T.59, E:T.59, E:G.60, E:K.61, E:T.62, E:T.62, E:T.63, E:T.63 Salt bridges: E:R.21, E:K.61, E:R.210 pi-Stacking: E:F.209

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marcus, K. et al., Autoinhibition of a clamp-loader ATPase revealed by deep mutagenesis and cryo-EM. Nat.Struct.Mol.Biol. (2024)

Release Date

2023-12-13

Peptides

Sliding-clamp-loader small subunit: A
Sliding-clamp-loader large subunit: BCDE
Sliding clamp: FGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Sliding-clamp-loader small subunit

Sliding-clamp-loader large subunit

Sliding clamp

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