SMTL ID : 2ca9.1

apo-NIKR from helicobacter pylori in closed trans-conformation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-tetramer

Ligands

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

FMT.1: 6 residues within 4Å: Chain A: Y.72, H.74, N.80, H.101, C.107 Chain D: H.88 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:N.80, D:H.88 FMT.2: 4 residues within 4Å: Chain A: Q.76, R.82, R.131 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.76, A:R.82 FMT.3: 5 residues within 4Å: Chain A: K.137, L.138, T.139 Chain B: L.138, T.139 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.138 Water bridges: A:T.139 FMT.4: 4 residues within 4Å: Chain A: H.74, H.75, R.77 Chain D: H.88 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:H.88 Water bridges: A:R.77, A:R.77 FMT.7: 3 residues within 4Å: Chain B: R.82, D.85, I.86 No protein-ligand interaction detected (PLIP) FMT.8: 5 residues within 4Å: Chain B: Y.72, H.99, H.101, C.107 Chain C: T.97 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Y.72, B:Y.72, C:T.97 FMT.9: 6 residues within 4Å: Chain A: R.28, N.32, Y.34, L.40 Chain B: K.48, D.52 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.34, B:D.52 Water bridges: B:K.48 FMT.11: 6 residues within 4Å: Chain B: H.88 Chain C: Y.72, H.74, N.80, H.101, C.107 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Y.72, C:N.80, B:H.88 FMT.12: 4 residues within 4Å: Chain C: Q.76, R.82, R.131 Ligands: GOL.16 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.76, C:R.82 FMT.13: 5 residues within 4Å: Chain C: K.137, L.138, T.139 Chain D: L.138, T.139 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.138 Water bridges: C:T.139 FMT.14: 4 residues within 4Å: Chain B: H.88 Chain C: H.74, H.75, R.77 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Water bridges: C:R.77, B:D.85 Hydrogen bonds: B:H.88 FMT.17: 3 residues within 4Å: Chain D: R.82, D.85, I.86 1 PLIP interactions: 1 interactions with chain D Water bridges: D:D.85 FMT.18: 5 residues within 4Å: Chain A: T.97 Chain D: Y.72, H.99, H.101, C.107 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.72 FMT.19: 6 residues within 4Å: Chain C: R.28, N.32, Y.34, L.40 Chain D: K.48, D.52 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.52 Water bridges: D:K.48

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 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.6: 5 residues within 4Å: Chain A: R.82, G.129, L.130, R.131 Ligands: FMT.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.82, A:R.82, A:R.131 Water bridges: A:R.82, A:R.131 GOL.10: 5 residues within 4Å: Chain B: N.80, M.83, Q.87, H.99, E.109 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.72 Water bridges: B:N.80 GOL.15: 3 residues within 4Å: Chain C: R.82, I.86, L.130 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.82 Water bridges: C:D.85 GOL.16: 5 residues within 4Å: Chain C: R.82, G.129, L.130, R.131 Ligands: FMT.12 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.82, C:R.82, C:R.131 Water bridges: C:R.82, C:R.131 GOL.20: 5 residues within 4Å: Chain D: N.80, M.83, Q.87, H.99, E.109 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.72, D:Y.72, D:N.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dian, C. et al., Structural Basis of the Nickel Response in Helicobacter Pylori: Crystal Structures of Hpnikr in Apo and Nickel-Bound States. J.Mol.Biol. (2006)

Release Date

2006-07-17

Peptides

PUTATIVE NICKEL-RESPONSIVE REGULATOR: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

PUTATIVE NICKEL-RESPONSIVE REGULATOR

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