SMTL ID : 5d4u.2 (1 other biounit)

SAM-bound HcgC from Methanocaldococcus jannaschii

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.1: 21 residues within 4Å: Chain A: K.34, G.54, 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 Ligands: SO4.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Y.56, A:Y.56, A:L.57, A:I.78, A:G.122, A:E.139, A:T.185, A:T.185 Water bridges: A:K.34, A:K.34, A:W.58, A:E.124, A:M.186 Salt bridges: A:K.34 SAM.8: 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 Ligands: SO4.9 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:V.55, B:Y.56, B:Y.56, B:Y.56, B:L.57, B:W.58, B:I.78, B:G.122, B:E.139, 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

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

SO4.2: 7 residues within 4Å: Chain A: Y.56, G.184, T.185, M.186, T.187, E.217 Ligands: SAM.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:M.186, A:T.187, A:T.187 Water bridges: A:T.182, A:G.184, A:T.185, A:T.187 SO4.3: 4 residues within 4Å: Chain A: D.140, K.142, Y.156, K.172 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.156 Water bridges: A:K.142, A:Y.150, A:Y.150 Salt bridges: A:K.142, A:K.172 SO4.4: 3 residues within 4Å: Chain A: H.79, E.80, F.81 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.80, A:F.81 Salt bridges: A:H.79 SO4.5: 3 residues within 4Å: Chain A: D.225, H.227, K.228 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.227, A:K.228 SO4.6: 4 residues within 4Å: Chain A: R.214, E.232 Chain B: R.214, E.232 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.214, A:K.228, B:R.214 SO4.7: 5 residues within 4Å: Chain A: R.178, E.199, N.256, N.257, L.260 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.199 Salt bridges: A:R.178 SO4.9: 8 residues within 4Å: Chain A: Y.208 Chain B: Y.56, G.184, T.185, M.186, T.187, E.217 Ligands: SAM.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.184, B:M.186, B:T.187, B:E.217 Water bridges: B:T.185 SO4.10: 4 residues within 4Å: Chain B: I.78, H.79, E.80, F.81 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.80, B:F.81 Salt bridges: B:H.79 SO4.11: 5 residues within 4Å: Chain B: Y.35, R.39, M.65, K.68, Y.69 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.35, B:Y.69 Salt bridges: B:R.39, B:K.68 SO4.12: 6 residues within 4Å: Chain B: N.110, P.111, D.112, N.132, P.133, K.134 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.110, B:N.132, B:K.134

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
B

B
D

Uncharacterized protein MJ0489

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