SMTL ID : 2caj.1

NIKR FROM HELICOBACTER PYLORI IN CLOSED TRANS-CONFORMATION AND NICKEL BOUND TO 4 INTERMEDIARY SITES

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-tetramer

Ligands

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: R.82, I.86 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.82 GOL.2: 6 residues within 4Å: Chain A: L.130, R.131, G.132, V.133, K.134 Chain B: R.46 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.130, A:G.132, B:R.46 GOL.3: 7 residues within 4Å: Chain A: N.80, M.83, Q.87, T.97, H.99, E.109, I.111 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.80 Water bridges: A:H.99 GOL.4: 6 residues within 4Å: Chain A: H.93, V.94, L.95 Chain D: I.100, H.101 Ligands: GOL.13 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.101, D:H.101 GOL.5: 7 residues within 4Å: Chain B: N.80, M.83, I.84, Q.87, T.97, H.99, E.109 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.80, B:E.109 Water bridges: B:T.97 GOL.6: 7 residues within 4Å: Chain B: H.74, H.75, R.77 Chain C: Q.81, I.84, D.85, H.88 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:Q.81, C:D.85, C:H.88, B:H.75, B:R.77 Water bridges: B:E.78, B:N.80 GOL.10: 2 residues within 4Å: Chain C: R.82, I.86 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.82 GOL.11: 6 residues within 4Å: Chain C: L.130, R.131, G.132, V.133, K.134 Chain D: R.46 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.46, C:L.130, C:G.132 GOL.12: 7 residues within 4Å: Chain C: N.80, M.83, Q.87, T.97, H.99, E.109, I.111 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.80, C:T.97 Water bridges: C:H.99 GOL.13: 6 residues within 4Å: Chain B: I.100, H.101 Chain C: H.93, V.94, L.95 Ligands: GOL.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.101, B:H.101 GOL.14: 7 residues within 4Å: Chain D: N.80, M.83, I.84, Q.87, T.97, H.99, E.109 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.80, D:E.109 GOL.15: 7 residues within 4Å: Chain A: Q.81, I.84, D.85, H.88 Chain D: H.74, H.75, R.77 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:Q.81, A:H.88, D:H.75, D:R.77 Water bridges: D:Q.76, D:E.78

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 5 residues within 4Å: Chain B: Q.87, H.93, V.94 Chain C: H.101 Ligands: NI.8 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain A: H.101 Chain D: Q.87, H.93, V.94 Ligands: NI.17 Ligand excluded by PLIP

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

NI.8: 3 residues within 4Å: Chain B: H.88 Chain C: H.74 Ligands: CL.7 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Metal complexes: B:H.88, C:H.74 NI.9: 4 residues within 4Å: Chain B: H.74, H.75, H.101 Chain C: H.88 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Metal complexes: B:H.74, C:H.88 NI.17: 3 residues within 4Å: Chain A: H.74 Chain D: H.88 Ligands: CL.16 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Metal complexes: D:H.88, A:H.74 NI.18: 4 residues within 4Å: Chain A: H.88 Chain D: H.74, H.75, H.101 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Metal complexes: A:H.88, D:H.74

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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