SMTL ID : 1n5w.1

Crystal Structure of the Cu,Mo-CO Dehydrogenase (CODH); Oxidized form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-2-2-2-mer

Ligands

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 1 residues within 4Å: Chain A: H.5 4 PLIP interactions: 4 interactions with chain A Water bridges: A:H.5, A:N.70, A:N.70 Salt bridges: A:H.5

4 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.2: 9 residues within 4Å: Chain A: L.100, Q.101, C.102, G.103, C.105, C.137, R.138, C.139 Chain B: L.217 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.102, A:C.105, A:C.137, A:C.139 FES.3: 10 residues within 4Å: Chain A: I.40, G.41, C.42, S.45, H.46, C.47, G.48, C.50, K.60, C.62 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.42, A:C.47, A:C.50, A:C.62 FES.7: 9 residues within 4Å: Chain D: L.100, Q.101, C.102, G.103, C.105, C.137, R.138, C.139 Chain E: L.217 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.102, D:C.105, D:C.137, D:C.139 FES.8: 10 residues within 4Å: Chain D: I.40, G.41, C.42, S.45, H.46, C.47, G.48, C.50, K.60, C.62 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.42, D:C.47, D:C.50, D:C.62

2 x CUM: CU(I)-S-MO(VI)(=O)OH CLUSTER(Non-covalent)

CUM.4: 13 residues within 4Å: Chain B: Q.240, F.271, G.272, V.384, A.385, Y.386, R.387, C.388, S.389, Y.568, G.569, E.763 Ligands: MCN.5 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Hydrogen bonds: B:Q.240, B:G.569 Water bridges: B:F.271, B:S.389 Metal complexes: B:C.388, H2O.23 CUM.9: 13 residues within 4Å: Chain E: Q.240, F.271, G.272, V.384, A.385, Y.386, R.387, C.388, S.389, Y.568, G.569, E.763 Ligands: MCN.10 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Hydrogen bonds: E:Q.240, E:G.569 Metal complexes: E:C.388, H2O.71

2 x MCN: PTERIN CYTOSINE DINUCLEOTIDE(Non-covalent)

MCN.5: 36 residues within 4Å: Chain A: Q.101, C.139 Chain B: G.269, G.270, F.271, G.272, R.387, Q.528, G.529, Q.530, G.531, H.532, T.535, T.567, Y.568, G.569, S.570, R.571, S.572, T.573, P.574, C.686, T.688, R.689, I.690, N.691, I.694, I.695, Q.698, A.758, K.759, G.760, V.761, G.762, E.763 Ligands: CUM.4 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.761 Hydrogen bonds: B:G.270, B:F.271, B:T.535, B:T.535, B:S.572, B:S.572, B:T.573, B:T.573, B:T.688, B:I.690, B:N.691, B:Q.698, B:K.759, B:V.761, B:G.762, A:Q.101 Water bridges: B:R.387, B:R.387, B:Q.528 Salt bridges: B:H.532 MCN.10: 35 residues within 4Å: Chain D: Q.101, C.139 Chain E: G.269, G.270, F.271, G.272, R.387, Q.528, G.529, Q.530, G.531, H.532, T.535, T.567, Y.568, G.569, S.570, R.571, S.572, T.573, C.686, T.688, R.689, I.690, N.691, I.694, I.695, Q.698, A.758, K.759, G.760, V.761, G.762, E.763 Ligands: CUM.9 25 PLIP interactions: 24 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:V.761 Hydrogen bonds: E:G.270, E:F.271, E:Q.530, E:T.535, E:S.572, E:S.572, E:S.572, E:T.573, E:T.573, E:T.688, E:I.690, E:N.691, E:Q.698, E:K.759, E:V.761, E:G.762, D:Q.101 Water bridges: E:R.387, E:R.387, E:Q.528, E:T.535, E:T.535, E:T.535 Salt bridges: E:H.532

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.6: 14 residues within 4Å: Chain A: S.45, H.46 Chain C: H.35, L.100, I.101, A.102, I.106, N.115, N.123, D.124, K.185, G.191, D.192, Y.193 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:A.102, C:I.106 Hydrogen bonds: C:A.102, C:N.115, C:N.123, C:D.124, C:D.124, C:D.124, C:K.185, C:Y.193 pi-Stacking: C:Y.193 FAD.11: 14 residues within 4Å: Chain D: S.45, H.46 Chain F: H.35, L.100, I.101, A.102, I.106, N.115, N.123, D.124, K.185, G.191, D.192, Y.193 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:A.102, F:I.106 Hydrogen bonds: F:A.102, F:N.115, F:D.124, F:D.124, F:K.185, F:Y.193

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dobbek, H. et al., Catalysis at a dinuclear [CuSMo(=O)OH] cluster in a CO dehydrogenase resolved at 1.1-A resolution. Proc.Natl.Acad.Sci.USA (2002)

Release Date

2002-12-23

Peptides

Carbon monoxide dehydrogenase small chain: AD
Carbon monoxide dehydrogenase large chain: BE
Carbon monoxide dehydrogenase medium chain: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

Carbon monoxide dehydrogenase small chain

Carbon monoxide dehydrogenase large chain

Carbon monoxide dehydrogenase medium chain

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