SMTL ID : 8rcg.1

W-formate dehydrogenase M405S from Desulfovibrio vulgaris

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 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: 37 residues within 4Å: Chain A: C.53, 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, S.405, G.406, W.407, H.410, 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 26 PLIP interactions: 26 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:S.405, A:S.405, A:S.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:D.275 Salt bridges: A:D.254, A:D.275, A:R.884, A:R.884, A:K.996 MGD.2: 33 residues within 4Å: Chain A: A.164, Q.188, I.191, U.192, Q.409, 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, G.892, L.893, M.894, W.964, N.979, T.995, K.996 Ligands: MGD.1, H2S.4, W.5, EDO.10 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:Q.188, A:Q.409, A:N.554, A:N.554, A:G.558, A:V.578, A:N.579, 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:K.996 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 SF4.12: 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 SF4.13: 14 residues within 4Å: Chain B: C.74, R.75, H.76, C.77, P.80, 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 SF4.14: 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: 8 residues within 4Å: Chain A: Q.188, U.192, 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)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: R.206, G.207, A.208, Y.462, W.492, W.765 Ligands: PEG.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.207 GOL.8: 11 residues within 4Å: Chain A: N.228, E.231, R.256, 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:R.884, A:R.946 Water bridges: A:R.884 GOL.9: 10 residues within 4Å: Chain A: V.74, E.75, G.76, G.85, L.87, A.92 Chain B: A.21, Q.24, K.155, T.156 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.24, A:G.76 Water bridges: B:T.156, A:E.75 GOL.11: 3 residues within 4Å: Chain A: K.361, H.362, R.365 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.365, A:R.365

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

PEG.7: 11 residues within 4Å: Chain A: R.206, W.491, F.714, W.728, L.729, W.765, P.766, R.769, I.817, M.818 Ligands: GOL.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.206, A:R.769, A:R.769

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

EDO.10: 6 residues within 4Å: Chain A: C.51, A.164, S.444, V.618, R.628 Ligands: MGD.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.444, A:S.444, A:R.628, A:R.628 Water bridges: A:S.611

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vilela-Alves, G. et al., Structural and biochemical characterization of the M405S variant of Desulfovibrio vulgaris formate dehydrogenase. Acta Crystallogr.,Sect.F (2024)

Release Date

2024-05-08

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

Related Entries With Identical Sequence