SMTL ID : 2wvf.1

Structural and mechanistic insights into Helicobacter pylori NikR function

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 1 residues within 4Å: Chain A: H.101 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.101, H2O.3 NI.11: 3 residues within 4Å: Chain B: H.99, H.101, C.107 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.99, B:H.101, B:C.107

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: E.78, R.82, D.85 Ligands: FMT.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.78 GOL.3: 1 residues within 4Å: Chain A: R.122 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.122 Water bridges: A:R.122 GOL.12: 6 residues within 4Å: Chain B: N.80, M.83, Q.87, T.97, E.109, I.111 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.80, B:M.83, B:T.97, B:T.97, B:E.109 GOL.13: 4 residues within 4Å: Chain A: S.142 Chain B: I.71, N.106, K.134 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.142 Water bridges: A:A.141, A:S.142

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

FMT.4: 2 residues within 4Å: Chain A: E.78 Ligands: GOL.2 No protein-ligand interaction detected (PLIP) FMT.5: 4 residues within 4Å: Chain A: I.84, Q.87, T.97, H.99 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.87 Water bridges: A:N.80, A:H.99 FMT.6: 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 FMT.7: 4 residues within 4Å: Chain A: L.138, T.139, K.140 Chain B: F.135 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.138, A:K.140 FMT.8: 2 residues within 4Å: Chain A: R.37 Chain B: I.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.37, A:R.37 FMT.14: 5 residues within 4Å: Chain A: N.32, Y.34, L.40, M.44 Chain B: D.52 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.34, A:Y.34 FMT.15: 3 residues within 4Å: Chain B: H.101, D.103, E.104 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.101

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

SO4.9: 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 SO4.10: 4 residues within 4Å: Chain A: S.90, G.91, E.119, R.122 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.91, A:E.119 Water bridges: A:E.119, A:R.122, A:R.122 Salt bridges: A:R.122

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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