SMTL ID : 3u5z.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

hetero-oligomer

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(Covalent)(Non-covalent)

08T.1: 20 residues within 4Å: Chain A: E.17, Q.18, 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 B: E.131, R.156 Ligands: MG.2 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.29, A:G.58, A:T.59, A:T.59, A:T.59, A:G.60, A:K.61, A:T.62, A:T.62, A:T.63, A:T.63, B:E.131 Salt bridges: A:R.21, A:K.61, A:R.210, A:R.210 08T.3: 21 residues within 4Å: Chain B: 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, R.180, F.209, R.210, I.213 Chain C: E.131, R.156 Ligands: MG.4 15 PLIP interactions: 15 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 08T.5: 21 residues within 4Å: Chain C: 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 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:T.59, C:G.60, C:K.61, C:T.62, 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: 7 residues within 4Å: Chain A: T.62, D.112, E.113, R.210 Chain B: E.131, R.156 Ligands: 08T.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.62, A:E.113 MG.4: 6 residues within 4Å: Chain B: T.62, D.112, E.113 Chain C: E.131, R.156 Ligands: 08T.3 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Metal complexes: B:T.62, B:E.113, C:E.131 MG.6: 6 residues within 4Å: Chain C: T.62, D.112, E.113 Chain D: E.131, R.156 Ligands: 08T.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.62, 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(Non-covalent)

ADP.7: 17 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, F.209, R.210, I.213 Ligands: MG.8 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:E.17, D:Y.20, D:I.29, D:G.58, D:T.59, D:T.59, D:T.59, D:G.60, D:K.61, D:T.62, D:T.62, D:T.63 Salt bridges: D:R.21, 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: E
DNA polymerase processivity component: FGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
M

C
N

D
O

E
K

F
Q

G
R

H
P

DNA polymerase accessory protein 44

DNA polymerase accessory protein 62

DNA polymerase processivity component

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