SMTL ID : 2wve.1

Structural and mechanistic insights into Helicobacter pylori NikR function

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: H.93, V.94 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.94 Salt bridges: A:H.93 SO4.2: 4 residues within 4Å: Chain A: S.35, S.36, E.39, R.42 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.35, A:S.36, A:S.36 Salt bridges: A:R.42 SO4.7: 2 residues within 4Å: Chain B: R.42, R.46 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.46 Salt bridges: B:R.42, B:R.46 SO4.8: 2 residues within 4Å: Chain B: S.36, R.37 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.37 Water bridges: B:S.36, B:R.37, B:R.37, B:S.38, B:S.38 Salt bridges: B:R.37 SO4.9: 5 residues within 4Å: Chain A: S.16 Chain B: S.36, S.38, E.39, R.42 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.36, B:E.39 Water bridges: B:S.35, B:S.38, B:R.42, A:S.16 Salt bridges: B:R.42

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: K.48, E.51, K.137, K.140 Chain B: R.28, N.32 Ligands: GOL.10 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.51, A:K.137, A:K.137, A:K.140, A:K.140, B:R.28, B:R.28, B:N.32 GOL.4: 5 residues within 4Å: Chain A: G.128, V.133, K.134, F.135, A.136 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.133, A:A.136, A:A.136 Water bridges: A:Q.124 GOL.10: 9 residues within 4Å: Chain A: K.48, Q.124, K.137 Chain B: R.28, Y.34, D.43, M.44, E.47 Ligands: GOL.3 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.124, A:K.137, A:K.137, B:R.28, B:Y.34 Water bridges: B:N.32

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.5: 4 residues within 4Å: Chain A: H.74, H.75, H.101, E.104 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.75, A:D.103 Water bridges: A:H.101

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.6: 6 residues within 4Å: Chain A: Y.72, H.74, N.80, H.99, H.101, C.107 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.72, A:N.80 Salt bridges: A:H.74, A:H.99, A:H.99, A:H.101, A:H.101

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