SMTL ID : 5a9k.1

Structural basis for DNA strand separation by a hexameric replicative helicase

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 19.00 Å

Oligo State

homo-hexamer

Ligands

9 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 8 residues within 4Å: Chain A: P.135, N.136, T.137, G.138, K.139, S.140 Ligands: PO4.2, MG.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.136, A:T.137, A:G.138, A:S.140 Salt bridges: A:K.139 PO4.2: 8 residues within 4Å: Chain A: P.135, N.136, K.139, D.179, N.223 Chain B: R.238 Ligands: PO4.1, MG.3 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.237, A:N.136, A:N.223 Salt bridges: B:R.238, A:K.139 PO4.4: 9 residues within 4Å: Chain B: N.136, T.137, G.138, K.139, S.140, M.141 Chain C: Y.199 Ligands: PO4.5, MG.6 10 PLIP interactions: 2 interactions with chain C, 8 interactions with chain B Hydrogen bonds: C:Y.199, C:Y.199, B:N.136, B:T.137, B:T.137, B:G.138, B:K.139, B:S.140, B:M.141 Salt bridges: B:K.139 PO4.5: 9 residues within 4Å: Chain B: P.135, N.136, K.139, D.179, N.223 Chain C: S.237, R.238 Ligands: PO4.4, MG.6 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:S.237, B:N.136, B:S.140, B:N.223 Salt bridges: C:R.238, B:K.139 PO4.7: 8 residues within 4Å: Chain C: N.136, T.137, G.138, K.139, S.140, M.141 Ligands: PO4.8, MG.9 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.136, C:T.137, C:T.137, C:K.139, C:S.140, C:M.141 Salt bridges: C:K.139 PO4.8: 9 residues within 4Å: Chain C: P.135, N.136, K.139, D.179, N.223 Chain D: S.237, R.238 Ligands: PO4.7, MG.9 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:N.136, C:S.140, C:N.223, D:S.237, D:S.237 Salt bridges: C:K.139, D:R.238 PO4.10: 9 residues within 4Å: Chain D: P.135, N.136, T.137, G.138, K.139, S.140, M.141 Chain E: Y.234, R.238 11 PLIP interactions: 8 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:N.136, D:T.137, D:T.137, D:G.138, D:K.139, D:S.140, D:M.141, E:Y.234, E:Y.234, E:R.238 Salt bridges: D:K.139 PO4.11: 8 residues within 4Å: Chain E: P.135, N.136, T.137, G.138, K.139, S.140, M.141 Chain F: Y.234 10 PLIP interactions: 9 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:N.136, E:T.137, E:G.138, E:K.139, E:S.140, E:S.140, E:S.140, E:M.141, F:Y.234 Salt bridges: E:K.139 PO4.12: 5 residues within 4Å: Chain F: N.136, T.137, G.138, K.139, S.140 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:N.136, F:T.137, F:G.138, F:K.139, F:S.140 Salt bridges: F:K.139

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: S.140, D.179 Chain B: R.238 Ligands: PO4.1, PO4.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.140, A:D.179 MG.6: 6 residues within 4Å: Chain B: S.140, D.179 Chain C: D.197, R.238 Ligands: PO4.4, PO4.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.140, B:D.179 MG.9: 5 residues within 4Å: Chain C: S.140, D.179 Chain D: R.238 Ligands: PO4.7, PO4.8 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:S.140, C:D.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chaban, Y. et al., Structural Basis for DNA Strand Separation by a Hexameric Replicative Helicase. Nucleic Acids Res. (2015)

Release Date

2015-08-26

Peptides

REPLICATION PROTEIN E1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

REPLICATION PROTEIN E1

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