SMTL ID : 4jjf.1

Crystal structure of FE-hydrogenase from methanothermobacter marburgensis in complex with 2-naphthylisocyanide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x FE9: IRON-GUANYLYL PYRIDINOL COFACTOR(Non-covalent)

FE9.1: 27 residues within 4Å: Chain A: L.6, G.7, A.8, G.9, C.10, T.13, H.14, A.62, D.63, P.64, P.110, P.111, D.131, W.144, F.145, P.146, I.154, A.171, C.172, T.173, H.203, P.204, G.205, A.206, V.207, P.208 Ligands: N2I.2 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:W.144, A:W.144 Hydrogen bonds: A:A.8, A:G.9, A:G.9, A:C.10, A:C.10, A:H.14, A:A.62, A:C.172, A:A.206 Water bridges: A:S.42, A:S.42, A:K.147 Salt bridges: A:D.63, A:D.131 pi-Stacking: A:F.145 Metal complexes: A:C.172 FE9.3: 27 residues within 4Å: Chain B: L.6, G.7, A.8, G.9, C.10, T.13, H.14, A.62, D.63, P.64, V.65, P.110, P.111, D.131, W.144, F.145, P.146, I.154, A.171, C.172, H.203, P.204, G.205, A.206, V.207, P.208 Ligands: N2I.4 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:W.144, B:W.144, B:A.171 Hydrogen bonds: B:A.8, B:G.9, B:G.9, B:C.10, B:C.10, B:A.62, B:C.172, B:G.205, B:A.206, B:A.206, B:A.206 Water bridges: B:D.131 Salt bridges: B:D.63, B:D.131 pi-Stacking: B:F.145 Metal complexes: B:C.172

2 x N2I: N-(NAPHTHALEN-2-YL)METHANIMINE(Non-covalent)

N2I.2: 6 residues within 4Å: Chain A: C.172, G.205, A.206, V.207, C.252 Ligands: FE9.1 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.207 N2I.4: 6 residues within 4Å: Chain B: C.172, G.205, A.206, V.207, C.252 Ligands: FE9.3 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.207

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tamura, H. et al., Crystal structures of [fe]-hydrogenase in complex with inhibitory isocyanides: implications for the h2 -activation site. Angew.Chem.Int.Ed.Engl. (2013)

Release Date

2013-08-07

Peptides

5,10-methenyltetrahydromethanopterin hydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

5,10-methenyltetrahydromethanopterin hydrogenase

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