SMTL ID : 1svl.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 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 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.52, C:C.55, C:H.63 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 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.52, E:C.55, E:H.63, E:H.67 ZN.16: 4 residues within 4Å: Chain F: C.52, C.55, H.63, H.67 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.52, F:C.55, F:H.63

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.183, E.223 Ligands: ADP.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.183, H2O.2, H2O.3, H2O.3, H2O.3 MG.5: 4 residues within 4Å: Chain B: T.183 Chain C: R.248, D.249 Ligands: ADP.6 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.183, H2O.5, H2O.5, H2O.5, H2O.8 MG.8: 4 residues within 4Å: Chain C: T.183, E.223 Chain D: R.248 Ligands: ADP.9 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:T.183, H2O.6, H2O.9, H2O.9, H2O.9 MG.11: 3 residues within 4Å: Chain D: T.183, E.223 Ligands: ADP.12 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:T.183, H2O.11, H2O.12, H2O.12, H2O.12 MG.14: 4 residues within 4Å: Chain E: T.183 Chain F: R.248, D.249 Ligands: ADP.15 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:T.183, H2O.14, H2O.14, H2O.14, H2O.17 MG.17: 4 residues within 4Å: Chain A: R.248 Chain F: T.183, E.223 Ligands: ADP.18 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:T.183, H2O.15, H2O.18, H2O.18, H2O.18

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

ADP.3: 18 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, R.298, P.299, K.300, L.303, L.307, L.314 Chain B: K.168 Ligands: MG.2 18 PLIP interactions: 15 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.179, A:D.179, A:S.180, A:G.181, A:K.182, A:T.183, A:T.183, A:T.184, A:T.184, A:R.298, A:K.300 Water bridges: A:K.182, A:T.183, B:K.168 Salt bridges: A:K.182, B:K.168, B:K.168 pi-Stacking: A:W.143 ADP.6: 20 residues within 4Å: Chain B: W.143, L.147, P.177, I.178, D.179, S.180, G.181, K.182, T.183, T.184, R.298, P.299, K.300, L.303, K.304, L.307, L.314 Chain C: K.168, R.248 Ligands: MG.5 22 PLIP interactions: 5 interactions with chain C, 17 interactions with chain B Hydrogen bonds: C:K.168, B:D.179, B:D.179, B:S.180, B:S.180, B:G.181, B:K.182, B:T.183, B:T.183, B:T.184, B:K.300 Water bridges: C:R.248, C:R.248, B:K.182, B:T.183, B:T.277, B:N.279, B:R.298 Salt bridges: C:R.248, C:R.248, B:K.182 pi-Stacking: B:W.143 ADP.9: 19 residues within 4Å: Chain C: W.143, L.147, P.177, I.178, D.179, S.180, G.181, K.182, T.183, T.184, R.298, P.299, K.300, L.303, L.307, L.314 Chain D: K.168, R.248 Ligands: MG.8 18 PLIP interactions: 15 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:D.179, C:D.179, C:S.180, C:G.181, C:K.182, C:T.183, C:T.183, C:T.184, C:R.298, C:K.300, D:K.168 Water bridges: C:T.184, C:R.298, C:Q.320 Salt bridges: C:K.182, D:R.248, D:R.248 pi-Stacking: C:W.143 ADP.12: 18 residues within 4Å: Chain D: W.143, L.147, P.177, I.178, D.179, S.180, G.181, K.182, T.183, T.184, R.298, P.299, K.300, L.303, L.307, L.314 Chain E: K.168 Ligands: MG.11 17 PLIP interactions: 13 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:D.179, D:S.180, D:G.181, D:K.182, D:T.183, D:T.183, D:T.183, D:T.184, D:R.298, D:K.300 Water bridges: D:K.182, E:K.168, E:K.168 Salt bridges: D:K.182, E:K.168, E:K.168 pi-Stacking: D:W.143 ADP.15: 20 residues within 4Å: Chain E: W.143, L.147, P.177, I.178, D.179, S.180, G.181, K.182, T.183, T.184, R.298, P.299, K.300, L.303, K.304, L.307, L.314 Chain F: K.168, R.248 Ligands: MG.14 22 PLIP interactions: 16 interactions with chain E, 6 interactions with chain F 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.184, E:T.184, E:K.300, F:K.168 Water bridges: E:K.182, E:T.183, E:N.279, E:R.298, F:R.248, F:R.248, F:D.249 Salt bridges: E:K.182, F:R.248, F:R.248 pi-Stacking: E:W.143 ADP.18: 19 residues within 4Å: Chain A: K.168, R.248 Chain F: W.143, L.147, P.177, I.178, D.179, S.180, G.181, K.182, T.183, T.184, R.298, P.299, K.300, L.303, L.307, L.314 Ligands: MG.17 18 PLIP interactions: 15 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:D.179, F:S.180, F:G.181, F:K.182, F:T.183, F:T.183, F:T.184, F:T.184, F:R.298, F:K.300, A:K.168 Water bridges: F:T.184, F:R.298, F:Q.320 Salt bridges: F:K.182, A:R.248, A:R.248 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
A

E
B

F
C

large T antigen

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