SMTL ID : 3u60.1

Structure of T4 Bacteriophage Clamp Loader Bound To Open Clamp, DNA and ATP Analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.34 Å

Oligo State

hetero-4-1-3-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: 22 residues within 4Å: Chain A: 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, F.209, R.210, I.213 Chain B: E.131, R.156 Ligands: MG.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:Y.20, A:I.29, A:G.58, A:T.59, A:T.59, A:G.60, A:K.61, A:T.62, A:T.63, A:T.63, A:T.63 Salt bridges: A:R.21, A:K.61, A:R.210, A:R.210 08T.3: 22 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, F.209, R.210, I.213 Chain C: E.131, R.156 Ligands: MG.4 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:Y.20, B:I.29, B:G.58, B:T.59, B:T.59, B:G.60, B:K.61, B:T.62, B:T.63, 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 08T.5: 21 residues within 4Å: Chain C: 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, F.209, R.210 Chain D: E.131, R.156 Ligands: MG.6 16 PLIP interactions: 16 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, C:T.63 Salt bridges: C:R.21, C:K.61, C:R.210, C:R.210

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: T.62, D.112, E.113 Chain B: E.131, R.156 Ligands: 08T.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.62 MG.4: 6 residues within 4Å: Chain B: T.62, D.112, E.113 Chain C: E.131, R.156 Ligands: 08T.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.113 MG.6: 6 residues within 4Å: Chain C: T.62, D.112, E.113 Chain D: E.131, R.156 Ligands: 08T.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.113 MG.8: 5 residues within 4Å: Chain D: T.62, D.112, E.113, R.210 Ligands: ADP.7 No protein-ligand interaction detected (PLIP)

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Covalent)

ADP.7: 16 residues within 4Å: Chain D: E.17, R.21, P.22, I.29, P.57, G.58, T.59, G.60, K.61, T.62, T.63, E.113, F.209, R.210, I.213 Ligands: MG.8 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:E.17, D:I.29, D:G.58, D:T.59, D:T.59, D:G.60, D:T.62, D:T.63, D:T.63, D:E.113 Salt bridges: D:K.61, D:R.210, D:R.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kelch, B.A. et al., How a DNA polymerase clamp loader opens a sliding clamp. Science (2011)

Release Date

2012-01-04

Peptides

DNA polymerase accessory protein 44: ABCD
DNA polymerase accessory protein 62: G
DNA polymerase processivity component: HIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

D
E

G
A

H
G

I
H

J
F

DNA polymerase accessory protein 44

DNA polymerase accessory protein 62

DNA polymerase processivity component

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