SMTL ID : 6sdv.1

W-formate dehydrogenase from Desulfovibrio vulgaris - Formate reduced form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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, I.270, 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 27 PLIP interactions: 27 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:R.884, A:H.888, A:Q.890 Water bridges: A:K.90, A:K.90, A:S.227, A:N.228, A:H.233, A:W.407, A:W.407 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, U.192, M.405, 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, K.996 Ligands: MGD.1, W.4, H2S.5 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: A:Q.188, A:N.554, A:N.554, A:G.558, A:V.578, A:N.579, A:N.579, A:L.580, A:K.614, A:T.882, A:T.882, A:R.884, A:R.884, A:T.891, A:T.891, A:T.891, A:G.892, A:L.893, A:N.979, A:N.979, A:T.995 Water bridges: A:G.558, A:G.558, A:K.614, A:D.641 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: 12 residues within 4Å: Chain A: C.50, Y.52, C.53, V.55, 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 SF4.19: 12 residues within 4Å: Chain B: C.12, T.13, A.14, C.15, R.16, C.18, P.71, C.157, P.158, T.159, T.161, M.162 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.12, B:C.15, B:C.18, B:C.157 SF4.20: 13 residues within 4Å: Chain B: C.74, R.75, H.76, C.77, P.80, P.81, C.82, V.103, C.121, Y.123, I.125, P.126, K.137 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.74, B:C.77, B:C.82, B:C.121 SF4.21: 12 residues within 4Å: Chain B: F.5, C.22, K.26, K.51, Q.73, C.138, D.139, M.140, C.141, P.151, A.152, C.153 5 PLIP interactions: 5 interactions with chain B, Salt bridges: B:D.139 Metal complexes: B:C.22, B:C.138, B:C.141, B:C.153

1 x W: TUNGSTEN ION(Non-covalent)

W.4: 4 residues within 4Å: Chain A: U.192 Ligands: MGD.1, MGD.2, H2S.5 No protein-ligand interaction detected (PLIP)

1 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.5: 7 residues within 4Å: Chain A: Q.188, U.192, E.443, V.446 Ligands: MGD.1, MGD.2, W.4 No protein-ligand interaction detected (PLIP)

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: R.206, G.207, A.208, Y.462, W.492, W.765 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.207 Water bridges: A:Q.447, A:Q.447 GOL.7: 12 residues within 4Å: Chain A: N.228, E.231, R.256, T.258, R.259, Y.883, R.884, V.885, E.911, R.946 Chain B: H.39, W.67 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.228, A:R.256, A:R.256, A:R.259, A:R.259, A:E.911, A:R.946, A:R.946 GOL.8: 12 residues within 4Å: Chain A: Y.300, R.775, V.778, D.779, K.780, W.799, P.810, G.811, T.812, K.813, H.814, P.815 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.775, A:D.779, A:G.811, A:T.812, A:K.813, A:K.813, A:H.814 GOL.9: 7 residues within 4Å: Chain A: E.84, G.85, S.86, K.238 Chain B: L.150, K.155, C.157 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.84, A:K.238, A:K.238, B:K.155 GOL.10: 6 residues within 4Å: Chain A: D.674, K.685, K.688, L.689, Y.693, Q.710 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.685, A:Q.710 GOL.11: 7 residues within 4Å: Chain A: E.615, W.627, Y.629, T.684, F.734, N.739, A.742 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.629, A:Y.629, A:T.684, A:N.739 GOL.12: 5 residues within 4Å: Chain A: R.70, E.99, N.100, D.101, Y.635 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.99 GOL.13: 4 residues within 4Å: Chain A: K.131, K.134, K.135, E.659 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.131 Water bridges: A:K.134, A:K.134 GOL.14: 6 residues within 4Å: Chain A: Q.752, W.799, V.800, G.801, D.802, V.803 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.752, A:G.801 Water bridges: A:G.801 GOL.15: 9 residues within 4Å: Chain A: N.214, A.217, N.218, W.239, K.246, A.753, R.754, I.755, G.756 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.214, A:N.218, A:K.246

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.16: 6 residues within 4Å: Chain A: C.845, C.872, P.874, Y.876, P.877, M.999 1 PLIP interactions: 1 interactions with chain A Water bridges: A:P.877 NO3.17: 3 residues within 4Å: Chain A: Y.876, S.931, D.1001 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.931, A:S.931 Water bridges: A:R.875

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.18: 4 residues within 4Å: Chain A: K.118, V.120, T.121, F.124 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.118, A:T.121, A:T.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oliveira, A.R. et al., Towards the mechanistic understanding of enzymatic CO2 reduction. Acs Catalysis (2020)

Release Date

2020-03-11

Peptides

Formate dehydrogenase, alpha subunit, selenocysteine-containing,Formate dehydrogenase, alpha subunit, selenocysteine-containing,W-formate dehydrogenase - alpha subunit: 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, alpha subunit, selenocysteine-containing,W-formate dehydrogenase - alpha subunit

Formate dehydrogenase, beta subunit, putative

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