SMTL ID : 2iv2.1

Reinterpretation of reduced form of formate dehydrogenase H from E. coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

monomer

Ligands

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 12 residues within 4Å: Chain A: C.8, Y.10, C.11, S.13, G.14, C.15, L.41, C.42, K.44, G.45, P.182, I.183 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.8, A:C.11, A:C.15, A:C.42

1 x 2MD: GUANYLATE-O'-PHOSPHORIC ACID MONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,5,6,7,8A,9,10,10A-OCTAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL) ESTER(Non-covalent)

2MD.2: 29 residues within 4Å: Chain A: R.110, G.111, T.112, C.136, A.137, M.297, Q.335, M.401, G.402, E.403, D.404, T.408, D.409, A.410, Q.428, D.429, I.430, F.431, T.433, S.445, T.446, H.451, D.478, C.588, S.590, Y.678 Ligands: MGD.3, MO.4, UNX.5 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:R.110, A:G.111, A:Q.335, A:G.402, A:D.404, A:A.410, A:Q.428, A:S.445, A:S.445, A:R.581, A:S.590, A:Y.678 Water bridges: A:S.108, A:S.108, A:S.109, A:C.136, A:E.403, A:T.408, A:T.408, A:W.448 Salt bridges: A:D.429, A:D.478 pi-Stacking: A:Y.678 pi-Cation interactions: A:Y.678

1 x MGD: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE(Non-covalent)

MGD.3: 38 residues within 4Å: Chain A: C.11, K.44, F.173, G.174, Y.175, N.176, D.179, S.180, C.201, D.202, P.203, R.204, I.206, L.218, N.220, G.221, N.223, G.296, M.297, G.298, F.302, G.334, Q.335, S.578, T.579, V.580, R.581, E.582, V.583, H.585, Y.586, S.587, Y.651, Q.655, K.679 Ligands: 2MD.2, MO.4, UNX.5 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:G.174, A:N.176, A:S.180, A:S.180, A:C.201, A:R.204, A:R.204, A:N.220, A:G.221, A:N.223, A:N.223, A:M.297, A:R.581, A:R.581, A:E.582, A:H.585, A:S.587, A:S.587 Water bridges: A:K.44, A:K.44, A:S.578 Salt bridges: A:D.202, A:K.679 pi-Stacking: A:F.302, A:F.302

1 x MO: MOLYBDENUM ATOM(Non-functional Binders)

MO.4: 3 residues within 4Å: Ligands: 2MD.2, MGD.3, UNX.5 Ligand excluded by PLIP

1 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.5: 7 residues within 4Å: Chain A: A.137, M.297, G.334, Q.335 Ligands: 2MD.2, MGD.3, MO.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Raaijmakers, H.C.A. et al., Formate-Reduced E. Coli Formate Dehydrogenase H: The Reinterpretation of the Crystal Structure Suggests a New Reaction Mechanism. J.Biol.Inorg.Chem. (2006)

Release Date

2006-06-12

Peptides

Formate dehydrogenase H: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

Formate dehydrogenase H

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