SMTL ID : 8unh.1

Cryo-EM structure of T4 Bacteriophage Clamp Loader with Sliding Clamp

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-1-3-mer

Ligands

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

AGS.1: 22 residues within 4Å: Chain A: L.11, E.12, Y.15, R.16, P.17, C.23, I.24, L.25, P.52, G.53, T.54, G.55, K.56, T.57, T.58, D.107, N.139, R.175, F.204, R.205, I.208 Ligands: MG.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:E.12, A:I.24, A:G.53, A:G.55, A:K.56, A:T.57, A:T.57, A:T.58, A:R.175, A:R.205 Salt bridges: A:R.16, A:K.56, A:R.205 AGS.3: 23 residues within 4Å: Chain B: E.12, Q.13, Y.15, R.16, P.17, C.23, I.24, L.25, P.52, G.53, T.54, G.55, K.56, T.57, T.58, E.108, N.139, R.175, F.204, R.205, I.208, R.232 Ligands: MG.4 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:Y.15, B:I.24, B:G.53, B:T.54, B:G.55, B:K.56, B:K.56, B:K.56, B:T.57, B:T.57, B:T.58, B:E.108, B:N.139, B:R.175 Salt bridges: B:R.16, B:K.56, B:R.205, B:R.205

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: K.56, T.57, D.107, E.108 Ligands: AGS.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.108 MG.4: 3 residues within 4Å: Chain B: T.57, E.108 Ligands: AGS.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.57

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 large subunit: ABCD
Sliding-clamp-loader small subunit: E
Sliding clamp: FGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
E

C
C

D
D

E
A

F
G

G
H

H
F

Sliding-clamp-loader large subunit

Sliding-clamp-loader small subunit

Sliding clamp

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