SMTL ID : 2hf9.1 (1 other biounit)

Crystal structure of HypB from Methanocaldococcus jannaschii in the triphosphate form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: T.52, D.80, E.125 Chain B: K.158 Ligands: GSP.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.52, A:D.80, A:E.125, H2O.1 MG.4: 4 residues within 4Å: Chain B: T.52, D.80, E.125 Ligands: GSP.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.52, B:D.80, B:E.125, H2O.4

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 2 residues within 4Å: Chain A: H.105, H.109 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.105, A:H.109 ZN.5: 2 residues within 4Å: Chain B: H.105, H.109 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.105, B:H.109

2 x GSP: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE(Non-covalent)

GSP.3: 24 residues within 4Å: Chain A: I.47, G.48, S.49, G.50, K.51, T.52, L.53, D.80, R.83, E.125, N.172, K.173, D.175, L.176, S.204, L.205, K.206 Chain B: T.150, E.151, G.152, K.158, A.179, V.180 Ligands: MG.1 21 PLIP interactions: 18 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.48, A:G.50, A:K.51, A:K.51, A:T.52, A:L.53, A:E.125, A:N.172, A:K.173, A:L.205, A:K.206, B:K.158, B:A.179 Water bridges: A:T.52, A:T.52, A:E.125 Salt bridges: A:K.51, A:R.83, A:D.175, B:K.158 pi-Cation interactions: A:K.173 GSP.6: 26 residues within 4Å: Chain A: T.150, E.151, G.152, K.158, A.179, V.180 Chain B: A.46, I.47, G.48, S.49, G.50, K.51, T.52, L.53, D.80, R.83, E.125, G.128, N.172, K.173, D.175, L.176, S.204, L.205, K.206 Ligands: MG.4 23 PLIP interactions: 16 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:G.48, B:G.50, B:K.51, B:T.52, B:T.52, B:L.53, B:N.172, B:K.173, B:S.204, B:L.205, B:K.206, A:A.179 Water bridges: B:S.49, A:E.151, A:K.158, A:K.158, A:K.158, A:H.159, A:V.180 Salt bridges: B:K.51, B:R.83, B:D.175 pi-Cation interactions: B:K.173

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gasper, R. et al., Structural insights into HypB, a GTP-binding protein that regulates metal binding. J.Biol.Chem. (2006)

Release Date

2006-07-04

Peptides

Probable hydrogenase nickel incorporation protein hypB: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Probable hydrogenase nickel incorporation protein hypB

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