SMTL ID : 8rc9.1

W-formate dehydrogenase from Desulfovibrio vulgaris - Co-crystallized with Formate and Exposed to air for 2 h

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

hetero-1-1-mer

Ligands

2 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.1: 35 residues within 4Å: Chain A: K.90, U.192, M.225, G.226, S.227, N.228, E.231, N.232, H.233, V.253, D.254, P.255, R.256, T.258, S.272, G.273, D.275, A.404, M.405, G.406, W.407, G.442, Y.883, R.884, V.885, T.886, H.888, W.889, Q.890, H.965, K.996 Ligands: MGD.2, W.4, H2S.5, OXY.10 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:G.226, A:N.228, A:E.231, A:N.232, A:N.232, A:V.253, A:R.256, A:R.256, A:G.273, A:M.405, A:G.406, A:R.884, A:R.884, A:H.888, A:Q.890, A:Q.890 Water bridges: A:K.90, A:K.90 Salt bridges: A:D.275, A:R.884, A:R.884, A:K.996 MGD.2: 30 residues within 4Å: Chain A: A.164, Q.188, I.191, M.405, E.443, W.551, G.552, M.553, N.554, G.558, V.578, N.579, L.580, C.608, C.609, K.614, D.641, T.882, R.884, Q.890, T.891, L.893, M.894, W.964, N.979, T.995 Ligands: MGD.1, W.4, H2S.5, OXY.10 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:Q.188, A:E.443, A:N.554, A:N.554, A:G.558, A:V.578, A:N.579, A:K.614, A:T.882, A:R.884, A:R.884, A:T.891, A:T.891, A:G.892, A:N.979, A:N.979 Water bridges: A:L.893 Salt bridges: A:D.641 pi-Stacking: A:W.964, A:W.964 pi-Cation interactions: A:W.964

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

SF4.3: 11 residues within 4Å: Chain A: C.50, Y.52, C.53, G.56, C.57, L.87, C.88, K.90, G.91, P.234, I.235 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.50, A:C.53, A:C.57, A:C.88 SF4.11: 12 residues within 4Å: Chain B: C.11, T.12, A.13, C.14, R.15, C.17, P.70, C.156, P.157, T.158, T.160, M.161 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.11, B:C.14, B:C.17, B:C.156 SF4.12: 12 residues within 4Å: Chain B: C.73, R.74, C.76, P.79, P.80, C.81, V.102, C.120, Y.122, I.124, P.125, K.136 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.73, B:C.76, B:C.81, B:C.120 SF4.13: 12 residues within 4Å: Chain B: F.4, C.21, K.25, K.50, Q.72, C.137, D.138, M.139, C.140, P.150, A.151, C.152 5 PLIP interactions: 5 interactions with chain B, Salt bridges: B:D.138 Metal complexes: B:C.21, B:C.137, B:C.140, B:C.152

1 x W: TUNGSTEN ION(Non-functional Binders)

W.4: 4 residues within 4Å: Ligands: MGD.1, MGD.2, H2S.5, OXY.10 No protein-ligand interaction detected (PLIP)

1 x H2S: HYDROSULFURIC ACID(Non-functional Binders)

H2S.5: 4 residues within 4Å: Ligands: MGD.1, MGD.2, W.4, OXY.10 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: R.206, G.207, A.208, Y.462, W.765 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.207 Water bridges: A:R.206, A:Y.462 GOL.7: 9 residues within 4Å: Chain A: N.214, A.217, N.218, W.239, K.246, R.754, I.755, G.756, F.758 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.214, A:N.214, A:K.246, A:R.754

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 9 residues within 4Å: Chain A: N.228, E.231, R.256, Y.883, R.884, V.885, E.911, R.946 Chain B: H.38 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.228, A:R.256, A:R.256, A:R.884, A:E.911, A:R.946 EDO.9: 9 residues within 4Å: Chain A: Y.300, R.775, V.778, D.779, K.780, P.810, G.811, T.812, K.813 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.775, A:G.811, A:T.812, A:K.813, A:K.813

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.10: 7 residues within 4Å: Chain A: I.191, U.192, M.405 Ligands: MGD.1, MGD.2, W.4, H2S.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vilela-Alves, G. et al., Substrate-dependent oxidative inactivation of a W-dependent formate dehydrogenase involving selenocysteine displacement. Chem Sci (2024)

Release Date

2024-07-24

Peptides

Formate dehydrogenase, alpha subunit, selenocysteine-containing: A
Formate dehydrogenase, beta subunit, putative: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Formate dehydrogenase, alpha subunit, selenocysteine-containing

Formate dehydrogenase, beta subunit, putative

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