SMTL ID : 2wvc.1

Structural and mechanistic insights into Helicobacter pylori NikR function

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: R.82, I.86, L.130 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.82 Water bridges: A:D.85, A:D.85 GOL.2: 4 residues within 4Å: Chain A: R.82, G.129, L.130, R.131 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.82, A:R.82, A:R.131 Water bridges: A:G.129 GOL.3: 6 residues within 4Å: Chain A: L.138, T.139, K.140 Chain B: F.135, K.137 Ligands: FMT.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.140, A:K.140, A:K.140 GOL.9: 5 residues within 4Å: Chain B: M.83, Q.87, T.97, E.109, I.111 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.97, B:E.109 GOL.10: 6 residues within 4Å: Chain B: Q.124, G.128, V.133, K.134, F.135, A.136 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.124, B:V.133, B:A.136, B:A.136

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 5 residues within 4Å: Chain A: S.36, S.38, E.39, R.42 Chain B: S.16 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.36, A:S.36, A:S.38 Salt bridges: A:R.42 SO4.5: 4 residues within 4Å: Chain A: E.39, R.42, D.43, R.46 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.43 Salt bridges: A:R.42, A:R.46 SO4.11: 5 residues within 4Å: Chain B: G.74, H.99, H.101, D.103, C.107 4 PLIP interactions: 4 interactions with chain B Water bridges: B:G.74, B:D.103 Salt bridges: B:H.99, B:H.101 SO4.12: 3 residues within 4Å: Chain A: S.16 Chain B: S.38, R.42 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.36, A:S.16, A:S.16 Salt bridges: B:R.42

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

FMT.6: 5 residues within 4Å: Chain A: L.138, T.139 Chain B: L.138, T.139 Ligands: GOL.3 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.138 Water bridges: B:T.139 FMT.7: 2 residues within 4Å: Chain B: R.82, I.86 No protein-ligand interaction detected (PLIP) FMT.8: 1 residues within 4Å: Chain B: R.77 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.77 Water bridges: B:R.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bahlawane, C. et al., Structural and Mechanistic Insights Into Helicobacter Pylori Nikr Activation. Nucleic Acids Res. (2010)

Release Date

2010-01-19

Peptides

PUTATIVE NICKEL-RESPONSIVE REGULATOR: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PUTATIVE NICKEL-RESPONSIVE REGULATOR

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