SMTL ID : 3wb2.1

HcgB from Methanocaldococcus jannaschii in complex with the guanylyl-pyridinol product in a model reaction of [Fe]-hydrogenase cofactor biosynthesis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.44 Å

Oligo State

homo-tetramer

Ligands

4 x YGP: 5'-O-[(R)-[(3,6-dimethyl-2-oxo-1,2-dihydropyridin-4-yl)oxy](hydroxy)phosphoryl]guanosine(Non-covalent)

YGP.1: 16 residues within 4Å: Chain A: R.20, R.21, G.22, D.23 Chain B: K.50, D.77, R.102, G.103, R.104, G.111, S.132, H.135, E.137, D.138, I.139, R.142 22 PLIP interactions: 5 interactions with chain A, 17 interactions with chain B Hydrogen bonds: A:R.20, A:R.21, A:R.21, A:D.23, A:D.23, B:R.102, B:R.102, B:R.104, B:R.104, B:S.132, B:E.137, B:E.137 Hydrophobic interactions: B:R.104 Water bridges: B:K.86, B:K.86, B:K.86, B:S.112, B:S.112, B:S.132, B:I.139 Salt bridges: B:K.50, B:R.102 YGP.2: 19 residues within 4Å: Chain A: K.50, D.77, K.86, R.102, G.103, R.104, G.111, S.112, S.132, H.135, E.137, D.138, I.139, R.142 Chain B: R.20, R.21, G.22, D.23 Ligands: GDP.4 18 PLIP interactions: 15 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:R.104 Hydrogen bonds: A:R.102, A:R.102, A:R.104, A:R.104, A:S.132, A:E.137, A:E.137, A:I.139, B:R.20, B:D.23 Water bridges: A:N.47, A:K.86, A:K.86, B:R.21 Salt bridges: A:K.50, A:K.86, A:R.102 YGP.6: 15 residues within 4Å: Chain C: R.20, R.21, G.22, D.23 Chain D: D.77, K.86, R.102, G.103, R.104, G.111, S.132, H.135, E.137, I.139, R.142 22 PLIP interactions: 16 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:R.102, D:R.102, D:R.104, D:R.104, D:S.132, D:E.137, D:E.137, D:I.139, C:R.20, C:R.21, C:R.21, C:D.23, C:D.23, C:D.23 Water bridges: D:K.50, D:K.50, D:K.86, D:K.86, D:R.102, D:S.132 Salt bridges: D:K.86, D:R.102 YGP.7: 16 residues within 4Å: Chain C: K.50, D.77, R.102, G.103, R.104, G.111, S.112, S.132, H.135, E.137, I.139, R.142 Chain D: R.20, R.21, G.22, D.23 18 PLIP interactions: 5 interactions with chain D, 13 interactions with chain C Hydrogen bonds: D:R.20, D:R.21, D:R.21, D:D.23, D:D.23, C:R.102, C:R.102, C:R.104, C:R.104, C:S.132, C:E.137, C:E.137 Hydrophobic interactions: C:R.104 Water bridges: C:K.86, C:K.86, C:I.139, C:I.139 Salt bridges: C:K.50

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: T.73, D.77 Ligands: GDP.4 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain A: E.160 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.160, A:E.160, H2O.2, H2O.2

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.4: 10 residues within 4Å: Chain A: T.45, N.46, N.47, K.50, T.73, K.86, R.102 Chain B: R.21 Ligands: YGP.2, MG.3 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.45, A:N.46, A:N.46, A:N.47, A:N.47, A:R.102 Water bridges: A:Q.48, A:K.86, A:K.86, B:R.21 Salt bridges: A:K.50, A:K.50, A:K.86 pi-Cation interactions: B:R.21, B:R.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fujishiro, T. et al., Identification of the HcgB enzyme in [Fe]-hydrogenase-cofactor biosynthesis. Angew.Chem.Int.Ed.Engl. (2013)

Release Date

2014-02-05

Peptides

Uncharacterized protein MJ0488: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Uncharacterized protein MJ0488

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