SMTL ID : 5d4v.1 (1 other biounit)

HcgC with SAH and a guanylylpyridinol (GP) derivative

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 22 residues within 4Å: Chain A: K.34, G.54, V.55, Y.56, L.57, W.58, V.76, D.77, I.78, H.79, M.82, L.97, L.117, T.118, G.122, I.123, E.139, S.183, G.184, T.185, F.221 Chain B: I.10 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:V.55, A:Y.56, A:Y.56, A:L.57, A:I.78, A:H.79, A:L.117, A:E.139, A:T.185 Water bridges: A:G.122, A:E.124, A:M.186 Salt bridges: A:K.34 SAH.5: 20 residues within 4Å: Chain B: K.34, G.54, V.55, Y.56, L.57, W.58, V.76, D.77, I.78, H.79, M.82, L.97, L.117, T.118, G.122, I.123, E.139, G.184, T.185, F.221 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:V.55, B:Y.56, B:Y.56, B:Y.56, B:L.57, B:I.78, B:L.117, B:G.122, B:T.185, B:T.185 Water bridges: B:K.34, B:K.34, B:E.124, B:M.186 Salt bridges: B:K.34

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

SO4.2: 4 residues within 4Å: Chain A: I.78, H.79, E.80, F.81 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.78, A:E.80, A:F.81 Water bridges: A:N.224 Salt bridges: A:H.79 SO4.3: 3 residues within 4Å: Chain A: R.214, S.231, E.232 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.231 Water bridges: A:R.214, A:R.214, A:R.214, A:R.214, A:S.231, A:S.231 Salt bridges: A:R.214 SO4.4: 4 residues within 4Å: Chain A: Y.35, R.39, K.68, Y.69 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.35, A:Y.35, A:Y.69 Salt bridges: A:R.39, A:K.68 SO4.6: 4 residues within 4Å: Chain B: I.78, H.79, E.80, F.81 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.80, B:F.81 Water bridges: B:I.78 Salt bridges: B:H.79 SO4.7: 5 residues within 4Å: Chain B: Y.56, T.182, G.184, M.186, T.187 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Y.56, B:T.182, B:T.182, B:M.186, B:T.187 Water bridges: B:T.185, B:T.185, B:E.217 SO4.8: 3 residues within 4Å: Chain B: R.214, S.231, E.232 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.232 Water bridges: B:R.214, B:R.214, B:R.214, B:R.214 Salt bridges: B:R.214 SO4.9: 5 residues within 4Å: Chain B: D.140, K.142, Y.156, K.172 Ligands: YGP.12 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.156 Water bridges: B:K.142, B:Y.150 Salt bridges: B:K.142, B:K.172 SO4.10: 1 residues within 4Å: Chain B: R.22 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.28 Salt bridges: B:R.22 SO4.11: 1 residues within 4Å: Chain B: H.227 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.227

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

YGP.12: 6 residues within 4Å: Chain B: Y.150, Y.156, K.157, A.160, E.266 Ligands: SO4.9 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:A.160 Hydrogen bonds: B:Y.156 Water bridges: B:K.142, B:Y.150, B:E.266 Salt bridges: B:K.157, B:E.266 pi-Stacking: B:Y.156, B:Y.156 pi-Cation interactions: B:Y.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fujishiro, T. et al., Identification of HcgC as a SAM-Dependent Pyridinol Methyltransferase in [Fe]-Hydrogenase Cofactor Biosynthesis. Angew.Chem.Int.Ed.Engl. (2016)

Release Date

2016-07-20

Peptides

Uncharacterized protein MJ0489: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Uncharacterized protein MJ0489

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