SMTL ID : 3dmn.1

The crystal structure of the C-terminal domain of a possilbe DNA helicase from Lactobacillus plantarun WCFS1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

monomer

Ligands

11 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 6 residues within 4Å: Chain A: N.124, Q.125, E.126, V.153, G.154, S.155 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.124, A:Q.125, A:E.126, A:S.155 Water bridges: A:E.126 ACT.2: 4 residues within 4Å: Chain A: K.82, E.86, Q.87, V.88 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.88 Salt bridges: A:K.82 ACT.3: 4 residues within 4Å: Chain A: L.19, V.20, N.21, R.134 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.19 Hydrogen bonds: A:V.20 Water bridges: A:Q.135 ACT.4: 3 residues within 4Å: Chain A: K.69, E.73, N.127 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.126, A:N.127 Water bridges: A:E.73 Salt bridges: A:K.69 ACT.5: 5 residues within 4Å: Chain A: T.78, K.82, V.88, T.89, L.90 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.78, A:L.90 Hydrogen bonds: A:L.90 Water bridges: A:Q.92 Salt bridges: A:K.82 ACT.6: 6 residues within 4Å: Chain A: S.107, A.110, L.136, T.139, I.140, R.143 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.136, A:T.139, A:I.140 Water bridges: A:A.110 Salt bridges: A:R.143 ACT.7: 3 residues within 4Å: Chain A: E.75, A.76, K.79 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.79 Hydrogen bonds: A:E.75 Water bridges: A:E.75, A:E.75, A:A.76, A:A.76 ACT.8: 4 residues within 4Å: Chain A: V.38, Q.49, N.171, E.172 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.38, A:N.171 Water bridges: A:V.37, A:E.172, A:E.172 ACT.9: 4 residues within 4Å: Chain A: A.72, E.73, A.76 Ligands: ACT.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.76 Water bridges: A:A.72, A:E.73, A:E.73, A:A.76 ACT.10: 8 residues within 4Å: Chain A: F.43, E.73, A.76, W.121, N.122, N.127 Ligands: ACT.9, ACT.11 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.43 Hydrogen bonds: A:N.122, A:N.127 Water bridges: A:N.127 ACT.11: 5 residues within 4Å: Chain A: F.43, N.122, N.124, V.153 Ligands: ACT.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.153 Hydrogen bonds: A:N.122, A:N.124, A:V.153

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.12: 2 residues within 4Å: Chain A: E.131, D.132 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.132 Water bridges: A:E.131, A:D.132 EDO.13: 3 residues within 4Å: Chain A: V.39, G.154, S.155 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.155 Water bridges: A:N.171

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.14: 2 residues within 4Å: Chain A: K.79, A.83 No protein-ligand interaction detected (PLIP) FMT.15: 5 residues within 4Å: Chain A: D.58, T.63, T.64, G.101, V.102 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.64 Water bridges: A:T.64, A:T.64, A:I.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, K. et al., The crystal structure of the C-terminal domain of a possilbe DNA helicase from Lactobacillus plantarun WCFS1. To be Published

Release Date

2008-08-26

Peptides

Putative DNA helicase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Putative DNA helicase