SMTL ID : 1svm.1

Co-crystal structure of SV40 large T antigen helicase domain and ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-hexamer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.52, C.55, H.63, H.67 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.52, A:C.55, A:H.63, A:H.67 ZN.4: 4 residues within 4Å: Chain B: C.52, C.55, H.63, H.67 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.52, B:C.55, B:H.63, B:H.67 ZN.7: 4 residues within 4Å: Chain C: C.52, C.55, H.63, H.67 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.52, C:C.55, C:H.63, C:H.67 ZN.10: 4 residues within 4Å: Chain D: C.52, C.55, H.63, H.67 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.52, D:C.55, D:H.63, D:H.67 ZN.13: 4 residues within 4Å: Chain E: C.52, C.55, H.63, H.67 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.52, E:C.55, E:H.63 ZN.16: 4 residues within 4Å: Chain F: C.52, C.55, H.63, H.67 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.52, F:C.55, F:H.63, F:H.67

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.183, E.223 Chain F: D.252 Ligands: ATP.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.183, H2O.1, H2O.6, H2O.6 MG.5: 4 residues within 4Å: Chain B: T.183, E.223, D.224 Ligands: ATP.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.183, H2O.11, H2O.11, H2O.11 MG.8: 4 residues within 4Å: Chain B: R.290 Chain C: T.183, D.224 Ligands: ATP.9 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.183, H2O.11, H2O.12, H2O.16 MG.11: 5 residues within 4Å: Chain C: D.252 Chain D: T.183, E.223, D.224 Ligands: ATP.12 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.183, H2O.16, H2O.21, H2O.21 MG.14: 4 residues within 4Å: Chain E: T.183, E.223, D.224 Ligands: ATP.15 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:T.183, H2O.17, H2O.27, H2O.27 MG.17: 5 residues within 4Å: Chain E: D.252 Chain F: T.183, E.223, D.224 Ligands: ATP.18 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:T.183, H2O.27, H2O.27, H2O.32

6 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.3: 22 residues within 4Å: Chain A: W.143, L.147, P.177, I.178, D.179, S.180, G.181, K.182, T.183, T.184, D.224, N.279, R.298, P.299, K.300, L.303, K.304, L.307, L.314 Chain F: K.168, R.290 Ligands: MG.2 25 PLIP interactions: 16 interactions with chain A, 9 interactions with chain F Hydrogen bonds: A:D.179, A:D.179, A:S.180, A:S.180, A:G.181, A:K.182, A:T.183, A:T.184, A:N.279, A:N.279, A:K.300 Water bridges: A:K.182, A:T.183, F:R.290, F:R.290, F:R.290, F:R.290, F:R.290 Salt bridges: A:K.182, A:K.182, F:K.168, F:K.168, F:K.168, F:R.290 pi-Stacking: A:W.143 ATP.6: 22 residues within 4Å: Chain A: K.168, K.169, R.290 Chain B: L.147, P.177, I.178, D.179, S.180, G.181, K.182, T.183, T.184, D.224, N.279, R.298, P.299, K.300, L.303, K.304, L.307, L.314 Ligands: MG.5 27 PLIP interactions: 18 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:D.179, B:D.179, B:S.180, B:S.180, B:G.181, B:G.181, B:K.182, B:T.183, B:T.184, B:T.184, B:N.279, B:N.279, B:K.300, A:K.169 Water bridges: B:K.182, B:T.183, B:E.223, A:K.169, A:R.290, A:R.290, A:R.290 Salt bridges: B:K.182, B:K.182, A:K.168, A:K.168, A:K.168, A:R.290 ATP.9: 21 residues within 4Å: Chain B: K.168, R.290 Chain C: L.147, P.177, I.178, D.179, S.180, G.181, K.182, T.183, T.184, D.224, N.279, R.298, P.299, K.300, L.303, K.304, L.307, L.314 Ligands: MG.8 28 PLIP interactions: 19 interactions with chain C, 9 interactions with chain B Hydrogen bonds: C:D.179, C:S.180, C:S.180, C:G.181, C:K.182, C:T.183, C:T.183, C:T.183, C:T.184, C:T.184, C:N.279, C:N.279, C:K.300 Water bridges: C:K.182, C:D.224, C:Q.320, B:K.169, B:R.290, B:R.290, B:R.290, B:R.290 Salt bridges: C:K.182, C:K.182, B:K.168, B:K.168, B:K.168, B:R.290 pi-Stacking: C:W.143 ATP.12: 22 residues within 4Å: Chain C: K.168, R.290 Chain D: W.143, L.147, P.177, I.178, D.179, S.180, G.181, K.182, T.183, T.184, D.224, N.279, R.298, P.299, K.300, L.303, K.304, L.307, L.314 Ligands: MG.11 25 PLIP interactions: 17 interactions with chain D, 8 interactions with chain C Hydrogen bonds: D:D.179, D:S.180, D:S.180, D:G.181, D:K.182, D:T.183, D:T.183, D:T.183, D:T.184, D:T.184, D:N.279, D:N.279, D:K.300 Water bridges: D:D.224, C:R.290, C:R.290, C:R.290, C:R.290 Salt bridges: D:K.182, D:K.182, C:K.168, C:K.168, C:K.168, C:R.290 pi-Stacking: D:W.143 ATP.15: 22 residues within 4Å: Chain D: K.168, D.252, R.290 Chain E: L.147, P.177, I.178, D.179, S.180, G.181, K.182, T.183, T.184, D.224, N.279, R.298, P.299, K.300, L.303, K.304, L.307, L.314 Ligands: MG.14 26 PLIP interactions: 17 interactions with chain E, 9 interactions with chain D Hydrogen bonds: E:D.179, E:S.180, E:S.180, E:G.181, E:K.182, E:T.183, E:T.183, E:T.183, E:T.184, E:D.224, E:N.279, E:K.300 Water bridges: E:K.182, E:K.182, E:R.298, D:K.169, D:R.290, D:R.290, D:R.290, D:R.290 Salt bridges: E:K.182, E:K.182, D:K.168, D:K.168, D:K.168, D:R.290 ATP.18: 20 residues within 4Å: Chain E: K.168, R.290 Chain F: L.147, I.178, D.179, S.180, G.181, K.182, T.183, T.184, D.224, N.279, R.298, P.299, K.300, L.303, K.304, L.307, L.314 Ligands: MG.17 27 PLIP interactions: 19 interactions with chain F, 8 interactions with chain E Hydrogen bonds: F:D.179, F:D.179, F:S.180, F:S.180, F:G.181, F:K.182, F:T.183, F:T.183, F:T.183, F:T.184, F:D.224, F:N.279, F:K.300 Water bridges: F:K.182, F:K.182, F:D.224, E:R.248, E:R.290, E:R.290, E:R.290 Salt bridges: F:K.182, F:K.182, E:K.168, E:K.168, E:K.168, E:R.290 pi-Stacking: F:W.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gai, D. et al., Mechanisms of conformational change for a replicative hexameric helicase of SV40 large tumor antigen. Cell(Cambridge,Mass.) (2004)

Release Date

2004-10-19

Peptides

large T antigen: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

large T antigen

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