SMTL ID : 1h0h.2 (1 other biounit)

Tungsten containing Formate Dehydrogenase from Desulfovibrio Gigas

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x W: TUNGSTEN ION(Non-covalent)

W.1: 4 residues within 4Å: Chain A: U.158 Ligands: 2MD.2, MGD.3, UNX.4 No protein-ligand interaction detected (PLIP)

1 x 2MD: GUANYLATE-O'-PHOSPHORIC ACID MONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,5,6,7,8A,9,10,10A-OCTAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL) ESTER(Non-covalent)

2MD.2: 32 residues within 4Å: Chain A: A.130, Q.154, I.157, U.158, M.371, E.409, W.515, G.516, Q.517, N.518, P.519, S.522, V.542, N.543, I.544, C.572, A.573, K.578, D.605, T.854, R.856, Q.862, T.863, L.865, M.866, W.936, N.951, P.965, T.967 Ligands: W.1, MGD.3, UNX.4 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:Q.154, A:Q.517, A:N.518, A:S.522, A:S.522, A:V.542, A:N.543, A:T.854, A:T.854, A:R.856, A:R.856, A:T.863, A:T.863, A:N.951, A:N.951, A:T.967 Water bridges: A:A.573, A:K.578, A:K.578, A:D.605, A:G.864, A:G.864 Salt bridges: A:D.605 pi-Stacking: A:W.936, A:W.936 pi-Cation interactions: A:W.936

1 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.3: 35 residues within 4Å: Chain A: K.56, U.158, M.191, G.192, S.193, N.194, E.197, N.198, V.219, D.220, P.221, R.222, T.224, L.236, S.238, G.239, D.241, A.370, M.371, W.373, G.408, E.409, S.853, Y.855, R.856, V.857, T.858, H.860, W.861, Q.862, H.937, K.968 Ligands: W.1, 2MD.2, UNX.4 31 PLIP interactions: 31 interactions with chain A Hydrogen bonds: A:G.192, A:N.194, A:N.194, A:E.197, A:N.198, A:N.198, A:V.219, A:R.222, A:R.222, A:G.239, A:M.371, A:R.856, A:R.856, A:H.860, A:Q.862, A:Q.862 Water bridges: A:K.56, A:K.56, A:S.193, A:H.199, A:D.241, A:G.372, A:S.853, A:R.856, A:K.968 Salt bridges: A:D.220, A:D.241, A:R.856, A:R.856, A:K.968, A:K.968

1 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.4: 9 residues within 4Å: Chain A: Q.154, U.158, H.159, G.408, E.409, V.412 Ligands: W.1, 2MD.2, MGD.3 No protein-ligand interaction detected (PLIP)

4 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.5: 12 residues within 4Å: Chain A: C.17, Y.19, C.20, V.22, G.23, C.24, L.53, C.54, K.56, G.57, P.200, I.201 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.17, A:C.20, A:C.24, A:C.54 SF4.8: 13 residues within 4Å: Chain B: C.11, T.12, A.13, C.14, R.15, C.17, V.52, P.69, C.156, P.157, T.158, A.160, M.161 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.11, B:C.14, B:C.17, B:C.156 SF4.9: 12 residues within 4Å: Chain B: F.4, C.21, H.25, K.50, Q.71, C.137, D.138, M.139, C.140, P.150, A.151, C.152 5 PLIP interactions: 5 interactions with chain B, Salt bridges: B:D.138 Metal complexes: B:C.21, B:C.137, B:C.140, B:C.152 SF4.10: 12 residues within 4Å: Chain B: C.72, R.73, H.74, C.75, P.79, C.80, V.101, C.120, P.121, Y.122, P.125, K.136 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.72, B:C.75, B:C.80, B:C.120

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 6 residues within 4Å: Chain A: T.358, K.360, K.363, L.393, G.394, N.395 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.358, A:K.360, A:K.363, A:L.393, H2O.12

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.7: 6 residues within 4Å: Chain B: P.42, D.43, I.117, D.123, R.126, Y.211 4 PLIP interactions: 4 interactions with chain B Water bridges: B:Q.39 Salt bridges: B:D.43, B:D.123, B:D.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Raaijmakers, H.C.A. et al., Gene Sequence and the 1.8 A Crystal Structure of the Tungsten-Containing Formate Dehydrogenase from Desulfovibrio Gigas. Structure (2002)

Release Date

2003-02-20

Peptides

FORMATE DEHYDROGENASE SUBUNIT ALPHA: A
FORMATE DEHYDROGENASE SUBUNIT BETA: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

B
L

FORMATE DEHYDROGENASE SUBUNIT ALPHA

FORMATE DEHYDROGENASE SUBUNIT BETA

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