SMTL ID : 8cm5.1 (3 other biounits)

W-formate dehydrogenase C872A from Desulfovibrio vulgaris

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-1-1-mer

Ligands

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

PEG.1: 8 residues within 4Å: Chain A: V.197, G.205, R.206, G.207, A.208, Y.462, W.492, W.765 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.207, A:A.208

1 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.2: 7 residues within 4Å: Chain A: U.192, G.442, E.443, V.446 Ligands: W.3, MGD.4, MGD.5 No protein-ligand interaction detected (PLIP)

1 x W: TUNGSTEN ION(Non-covalent)

W.3: 5 residues within 4Å: Chain A: U.192, R.884 Ligands: H2S.2, MGD.4, MGD.5 No protein-ligand interaction detected (PLIP)

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.4: 35 residues within 4Å: Chain A: C.53, K.90, U.192, G.226, S.227, N.228, E.231, N.232, H.233, D.254, P.255, R.256, S.272, G.273, D.275, A.404, M.405, G.406, W.407, H.410, G.442, E.443, T.881, Y.883, R.884, V.885, T.886, H.888, W.889, Q.890, H.965, K.996 Ligands: H2S.2, W.3, MGD.5 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:G.226, A:N.228, A:E.231, A:N.232, A:N.232, A:R.256, A:R.256, A:G.273, A:M.405, A:G.406, A:W.407, A:T.881, A:R.884, A:R.884, A:H.888, A:Q.890, A:Q.890 Water bridges: A:K.90, A:K.90, A:N.228 Salt bridges: A:D.275, A:R.884, A:R.884, A:K.996 MGD.5: 33 residues within 4Å: Chain A: A.164, Q.188, I.191, U.192, M.405, 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, L.893, M.894, W.964, N.979, T.982, T.995, K.996 Ligands: H2S.2, W.3, MGD.4 26 PLIP interactions: 26 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:N.979, A:N.979, A:K.996 Water bridges: A:G.558, A:G.558, A:C.609, A:D.641, A:G.892, A:G.892 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)

SF4.6: 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 SF4.7: 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 SF4.8: 12 residues within 4Å: Chain B: C.74, R.75, H.76, C.77, 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 SF4.9: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oliveira, A.R. et al., An allosteric redox switch involved in oxygen protection in a CO 2 reductase. Nat.Chem.Biol. (2024)

Release Date

2023-09-27

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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