SMTL ID : 8uk9.2 (1 other biounit)

Structure of T4 Bacteriophage clamp loader mutant D110C bound to the T4 clamp, primer-template DNA, and ATP analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-4-1-3-mer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 7 residues within 4Å: Chain A: T.58, D.108, E.109 Chain B: E.127, R.152 Ligands: AF3.2, ADP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.109 MG.4: 7 residues within 4Å: Chain B: T.58, D.108, E.109 Chain C: E.127, R.152 Ligands: AF3.5, ADP.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.58, B:E.109 MG.7: 6 residues within 4Å: Chain C: T.58, D.108, E.109 Chain D: E.127 Ligands: AF3.8, ADP.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.58, C:E.109 MG.11: 3 residues within 4Å: Chain D: T.58, E.109 Ligands: ADP.10 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.58, D:E.109

3 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.2: 10 residues within 4Å: Chain A: P.53, G.54, K.57, T.58, E.109, N.140, R.206 Chain B: R.152 Ligands: MG.1, ADP.3 No protein-ligand interaction detected (PLIP) AF3.5: 10 residues within 4Å: Chain B: P.53, K.57, T.58, E.109, T.138, N.140, R.206 Chain C: R.152 Ligands: MG.4, ADP.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.109 AF3.8: 10 residues within 4Å: Chain C: P.53, K.57, T.58, E.109, T.138, N.140, R.206 Chain D: R.152 Ligands: MG.7, ADP.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.109

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

ADP.3: 20 residues within 4Å: Chain A: E.13, Y.16, R.17, P.18, C.24, I.25, P.53, G.54, T.55, G.56, K.57, T.58, T.59, E.109, R.176, F.205, R.206 Chain B: E.127 Ligands: MG.1, AF3.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:Y.16, A:R.17, A:I.25, A:G.54, A:T.55, A:T.55, A:G.56, A:K.57, A:T.58, A:R.176 Salt bridges: A:R.17, A:K.57, A:R.206, A:R.206 pi-Stacking: A:F.205 ADP.6: 22 residues within 4Å: Chain B: E.13, Q.14, Y.16, R.17, P.18, C.24, I.25, P.53, G.54, T.55, G.56, K.57, T.58, T.59, E.109, R.176, F.205, R.206, I.209 Chain C: E.127 Ligands: MG.4, AF3.5 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Y.16, B:R.17, B:I.25, B:G.54, B:T.55, B:T.55, B:G.56, B:K.57, B:T.58, B:T.58, B:T.59, C:R.152 Salt bridges: B:R.17, B:K.57, B:R.206, B:R.206 pi-Stacking: B:F.205, B:F.205 ADP.9: 22 residues within 4Å: Chain C: E.13, Q.14, Y.16, R.17, P.18, C.24, I.25, L.26, P.53, G.54, T.55, G.56, K.57, T.58, T.59, R.176, F.205, R.206, I.209 Chain D: E.127 Ligands: MG.7, AF3.8 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:Y.16, C:R.17, C:R.17, C:I.25, C:T.55, C:T.55, C:G.56, C:K.57, C:T.58, C:T.58, C:T.59 Salt bridges: C:R.17, C:K.57, C:R.206, C:R.206 pi-Stacking: C:F.205 ADP.10: 16 residues within 4Å: Chain D: E.13, Q.14, Y.16, R.17, P.18, I.25, G.54, T.55, G.56, K.57, T.58, T.59, F.205, R.206, I.209 Ligands: MG.11 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:Y.16, D:I.25, D:I.25, D:T.55, D:G.56, D:K.57, D:T.58, D:T.58, D:T.58, D:T.59 Salt bridges: D:R.206

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: G
Sliding clamp: HIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

B
L

C
M

D
N

G
Q

H
R

I
S

J
T

Sliding-clamp-loader large subunit

Sliding-clamp-loader small subunit

Sliding clamp

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