SMTL ID : 8bqh.1

W-formate dehydrogenase from Desulfovibrio vulgaris - Soaking with Formate 1.5 min

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.61 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: 36 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, E.443, Y.883, R.884, V.885, T.886, H.888, W.889, Q.890, H.965, K.996 Ligands: MGD.2, H2S.4, W.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:H.888, A:Q.890, A:Q.890 Water bridges: A:K.90, A:K.90, A:S.227, A:N.228, A:H.233, A:W.407, A:N.416 Salt bridges: A:D.275, A:R.884, A:R.884, A:K.996 MGD.2: 32 residues within 4Å: Chain A: A.164, Q.188, I.191, U.192, 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, W.889, Q.890, T.891, L.893, M.894, W.964, N.979, T.995, K.996 Ligands: MGD.1, H2S.4, W.5 28 PLIP interactions: 28 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:L.580, A:K.614, A:T.882, A:T.882, A:R.884, A:R.884, A:T.891, A:T.891, A:G.892, A:N.979, A:N.979, A:T.995, A:K.996 Water bridges: A:G.558, A:G.558, A:A.560, A:C.609, 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 SF4.27: 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 SF4.28: 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 SF4.29: 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 H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.4: 9 residues within 4Å: Chain A: Q.188, U.192, H.193, G.442, E.443, V.446 Ligands: MGD.1, MGD.2, W.5 No protein-ligand interaction detected (PLIP)

1 x W: TUNGSTEN ION(Non-covalent)

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

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.6: 13 residues within 4Å: Chain A: A.201, R.206, G.207, Y.462, W.491, W.492, F.714, W.728, L.729, W.765, P.766, R.769, M.818 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.206, A:G.207, A:R.769 PG4.7: 8 residues within 4Å: Chain A: D.101, Q.102, R.103, L.108, W.117, P.119, E.582 Ligands: EDO.16 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.582

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 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 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.228, A:R.256, A:R.256, A:R.259, A:R.259, A:R.884, A:E.911, A:R.946, A:R.946 GOL.9: 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.775, A:G.782, A:G.811, A:T.812, A:K.813, A:H.814

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

PEG.10: 5 residues within 4Å: Chain A: A.737, N.739, L.740, A.742, R.743 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.742 Water bridges: A:R.743 PEG.11: 5 residues within 4Å: Chain A: Q.907, T.927, E.938, N.973, G.975 6 PLIP interactions: 6 interactions with chain A Water bridges: A:Q.907, A:Q.907, A:E.938, A:E.938, A:E.938, A:E.938 PEG.15: 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 PEG.17: 4 residues within 4Å: Chain A: K.290, Y.292, T.294 Ligands: EDO.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.292, A:Y.292, A:T.294

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

EDO.12: 3 residues within 4Å: Chain A: Y.292 Ligands: EDO.13, PEG.17 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.360 EDO.13: 5 residues within 4Å: Chain A: Y.292, L.349, N.357, K.360 Ligands: EDO.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.292, A:N.357, A:K.360 EDO.14: 6 residues within 4Å: Chain A: I.60, H.62, E.75 Chain B: W.25, R.144, L.149 No protein-ligand interaction detected (PLIP) EDO.16: 6 residues within 4Å: Chain A: D.115, T.116, W.117, W.589, K.590 Ligands: PG4.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.117, A:K.590, A:K.590 Water bridges: A:W.117

5 x FMT: FORMIC ACID(Non-functional Binders)

FMT.18: 4 residues within 4Å: Chain A: L.740, R.743, F.763, N.768 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.743, A:R.743, A:N.768 Water bridges: A:P.759 FMT.19: 4 residues within 4Å: Chain A: R.875, Y.876, S.931, D.1001 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.931, A:S.931 Water bridges: A:S.931, A:R.1003 FMT.20: 7 residues within 4Å: Chain A: R.190, S.194, V.197, P.198, L.455, H.457 Ligands: FMT.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.190 FMT.21: 3 residues within 4Å: Chain A: H.457, Y.462 Ligands: FMT.20 No protein-ligand interaction detected (PLIP) FMT.30: 3 residues within 4Å: Chain A: A.899 Chain B: P.29, A.30 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.30, B:A.30, A:Q.96

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.22: 4 residues within 4Å: Chain A: A.64, K.65, G.69, R.70 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain A: R.653, L.670, I.672, A.673 Ligand excluded by PLIP CL.24: 5 residues within 4Å: Chain A: N.561, R.934, P.983, S.984, A.985 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain A: D.745, K.746 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain A: K.118, F.124 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vilela-Alves, G. et al., Tracking W-Formate Dehydrogenase Structural Changes During Catalysis and Enzyme Reoxidation. Int J Mol Sci (2022)

Release Date

2023-01-18

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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