SMTL ID : 2gxa.1 (1 other biounit)

Crystal structure of papillomavirus E1 hexameric helicase with ssDNA and MgADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

homo-hexamer

Ligands

5 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain B: S.137, D.176 Chain C: D.194, R.235 Ligands: CL.2, ADP.3 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.137, H2O.1, H2O.1, H2O.1 MG.4: 5 residues within 4Å: Chain C: S.137, D.176 Chain D: D.194, R.235 Ligands: ADP.6 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:S.137, C:D.176, H2O.1, H2O.1, H2O.1 MG.7: 5 residues within 4Å: Chain D: S.137, D.176 Chain E: D.194, R.235 Ligands: ADP.8 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:S.137, D:D.176, H2O.1, H2O.1, H2O.1 MG.9: 4 residues within 4Å: Chain E: S.137, D.176 Chain F: Y.231 Ligands: ADP.10 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.137 MG.11: 3 residues within 4Å: Chain F: S.137, D.176 Ligands: ADP.12 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.137

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 6 residues within 4Å: Chain B: P.132, K.136, D.176 Chain C: R.235 Ligands: MG.1, ADP.3 Ligand excluded by PLIP CL.5: 6 residues within 4Å: Chain C: P.132, K.136, D.176, N.220 Chain D: R.235 Ligands: ADP.6 Ligand excluded by PLIP

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

ADP.3: 14 residues within 4Å: Chain B: N.133, T.134, G.135, K.136, S.137, M.138, N.255 Chain C: I.120, P.121, K.122, K.123, Y.196 Ligands: MG.1, CL.2 17 PLIP interactions: 12 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:N.133, B:T.134, B:G.135, B:K.136, B:S.137, B:M.138, C:K.123, C:Y.196, C:R.235 Water bridges: B:K.136, B:S.137, B:S.137, B:D.176, B:D.176 Salt bridges: B:K.136, C:K.122, C:K.122 ADP.6: 16 residues within 4Å: Chain C: N.133, T.134, G.135, K.136, S.137, M.138, C.245, Q.252, N.255 Chain D: I.120, P.121, K.122, K.123, Y.196 Ligands: MG.4, CL.5 17 PLIP interactions: 11 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:N.133, C:N.133, C:T.134, C:G.135, C:K.136, C:S.137, C:M.138, D:K.123, D:K.123, D:Y.196 Water bridges: C:S.137, C:S.137, C:D.176, D:R.235 Salt bridges: C:K.136, D:K.122, D:K.122 ADP.8: 14 residues within 4Å: Chain D: P.132, N.133, T.134, G.135, K.136, S.137, M.138, T.246, Q.252, N.255 Chain E: P.121, K.122, Y.196 Ligands: MG.7 15 PLIP interactions: 11 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:N.133, D:N.133, D:T.134, D:G.135, D:K.136, D:S.137, D:M.138, E:Y.196 Water bridges: D:S.137, D:S.137, D:S.137, E:D.194 Salt bridges: D:K.136, E:K.122, E:K.122 ADP.10: 13 residues within 4Å: Chain E: N.133, T.134, G.135, K.136, S.137, M.138, T.246, Q.252, F.254, N.255 Chain F: Y.196, Y.231 Ligands: MG.9 11 PLIP interactions: 8 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:N.133, E:T.134, E:G.135, E:K.136, E:S.137, E:M.138, E:N.255, F:Y.196, F:Y.231, F:Y.231 Salt bridges: E:K.136 ADP.12: 14 residues within 4Å: Chain F: N.133, T.134, G.135, K.136, S.137, M.138, C.245, Q.252, F.254, N.255, I.256 Chain G: K.122, Y.196 Ligands: MG.11 11 PLIP interactions: 2 interactions with chain G, 9 interactions with chain F Hydrogen bonds: G:K.122, G:Y.196, F:N.133, F:T.134, F:G.135, F:K.136, F:S.137, F:M.138, F:N.255, F:I.256 Salt bridges: F:K.136 ADP.13: 12 residues within 4Å: Chain B: Y.196 Chain G: P.132, N.133, T.134, G.135, K.136, S.137, M.138, D.176, N.220, C.245, F.254 12 PLIP interactions: 11 interactions with chain G, 1 interactions with chain B Hydrogen bonds: G:N.133, G:T.134, G:G.135, G:K.136, G:S.137, G:S.137, G:M.138, G:D.176, G:N.220, B:Y.196 Salt bridges: G:K.136, G:K.136

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Enemark, E.J. et al., Mechanism of DNA translocation in a replicative hexameric helicase. Nature (2006)

Release Date

2006-07-25

Peptides

Replication protein E1: BCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

C
B

D
C

E
D

F
E

G
F

Replication protein E1

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