SMTL ID : 8rcc.1

W-formate dehydrogenase from Desulfovibrio vulgaris - aerobic soaked with 48 bar CO2 for 1 min

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 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, 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, H2S.4, W.5, CO2.12, OXY.31 21 PLIP interactions: 21 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 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, Q.890, T.891, L.893, M.894, W.964, N.979, T.995, K.996 Ligands: MGD.1, H2S.4, W.5, OXY.31 18 PLIP interactions: 18 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:K.614, A:T.882, A:R.884, A:R.884, A:T.891, A:N.979, A:N.979 Water bridges: A:S.611 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 SF4.33: 11 residues within 4Å: Chain B: C.12, T.13, A.14, C.15, R.16, C.18, P.71, C.157, 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 SF4.34: 13 residues within 4Å: Chain B: C.74, R.75, H.76, C.77, P.81, C.82, V.103, C.121, P.122, 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 SF4.35: 12 residues within 4Å: Chain B: F.5, C.22, K.26, L.50, K.51, 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, G.442, E.443, V.446 Ligands: MGD.1, MGD.2, W.5, CO2.12, OXY.31 No protein-ligand interaction detected (PLIP)

1 x W: TUNGSTEN ION(Non-covalent)

W.5: 5 residues within 4Å: Chain A: U.192 Ligands: MGD.1, MGD.2, H2S.4, OXY.31 No protein-ligand interaction detected (PLIP)

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 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.7: 7 residues within 4Å: Chain A: R.206, G.207, A.208, Y.462, W.492, W.765 Ligands: EDO.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.207 GOL.36: 7 residues within 4Å: Chain B: L.104, F.105, L.135, S.136, K.137, C.138, D.139 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.103, B:F.105

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

EDO.8: 9 residues within 4Å: Chain A: Y.300, R.775, V.778, D.779, P.810, G.811, K.813, H.814, P.815 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.775, A:G.811 EDO.10: 9 residues within 4Å: Chain A: N.214, A.217, N.218, W.239, K.246, R.754, I.755, G.756 Ligands: CO2.27 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.214, A:N.214, A:K.246, A:R.754 EDO.16: 3 residues within 4Å: Chain A: D.346, K.350, H.351 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.346, A:H.351 EDO.18: 6 residues within 4Å: Chain A: W.491, F.714, R.769, G.806, G.807, I.817 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.491, A:R.769, A:R.769, A:G.807 EDO.22: 5 residues within 4Å: Chain A: W.794, W.799, G.807, G.808, D.809 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.799, A:G.808 EDO.26: 7 residues within 4Å: Chain A: R.206, F.714, W.728, P.766, R.769, M.818 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.206, A:R.769 EDO.29: 6 residues within 4Å: Chain A: A.398, V.432, A.433, N.786, K.789, V.791 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.786, A:K.789 EDO.30: 5 residues within 4Å: Chain A: K.685, K.688, L.689, Y.693, Q.710 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.688, A:K.688 EDO.32: 4 residues within 4Å: Chain A: A.899, V.902 Chain B: E.31, E.32 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.32, B:E.32

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

PEG.9: 4 residues within 4Å: Chain A: Q.907, T.927, V.940 Chain B: R.34 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.34, A:Q.907, A:E.938

17 x CO2: CARBON DIOXIDE(Non-covalent)

CO2.11: 4 residues within 4Å: Chain A: R.190, H.193, S.194, H.457 Ligand excluded by PLIP CO2.12: 8 residues within 4Å: Chain A: U.192, L.440, R.441, G.442, V.446 Ligands: MGD.1, H2S.4, OXY.31 Ligand excluded by PLIP CO2.13: 8 residues within 4Å: Chain A: T.47, S.48, I.49, G.58, L.59, D.77, H.80, R.744 Ligand excluded by PLIP CO2.14: 1 residues within 4Å: Chain A: L.108 Ligand excluded by PLIP CO2.15: 6 residues within 4Å: Chain A: R.178, L.182, V.183, W.459, V.465, P.520 Ligand excluded by PLIP CO2.17: 3 residues within 4Å: Chain A: K.284, N.367, L.368 Ligand excluded by PLIP CO2.19: 3 residues within 4Å: Chain A: K.567, G.593, M.594 Ligand excluded by PLIP CO2.20: 5 residues within 4Å: Chain A: Y.876, S.932, G.935 Ligands: CO2.21, CO2.25 Ligand excluded by PLIP CO2.21: 3 residues within 4Å: Chain A: K.929, A.936 Ligands: CO2.20 Ligand excluded by PLIP CO2.23: 4 residues within 4Å: Chain A: K.854, Q.855, L.856, H.857 Ligand excluded by PLIP CO2.24: 2 residues within 4Å: Chain A: Y.321, Q.855 Ligand excluded by PLIP CO2.25: 3 residues within 4Å: Chain A: Y.876, S.931 Ligands: CO2.20 Ligand excluded by PLIP CO2.27: 5 residues within 4Å: Chain A: P.81, E.84, W.239, F.758 Ligands: EDO.10 Ligand excluded by PLIP CO2.28: 8 residues within 4Å: Chain A: G.341, V.342, P.343, S.483, K.484, D.485, T.820, H.821 Ligand excluded by PLIP CO2.37: 3 residues within 4Å: Chain B: L.28, Y.47, S.136 Ligand excluded by PLIP CO2.38: 7 residues within 4Å: Chain B: L.45, L.50, Q.73, C.74, I.125, K.137, C.138 Ligand excluded by PLIP CO2.39: 6 residues within 4Å: Chain B: T.56, K.58, K.207, D.208, Y.210, E.211 Ligand excluded by PLIP

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.31: 7 residues within 4Å: Chain A: Q.188, U.192 Ligands: MGD.1, MGD.2, H2S.4, W.5, CO2.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.188

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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