SMTL ID : 1n62.1

Crystal Structure of the Mo,Cu-CO Dehydrogenase (CODH), n-butylisocyanide-bound state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.09 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 3 PLIP interactions: 3 interactions with chain A Water bridges: 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 CUB: CU(I)-S-MO(IV)(=O)O-NBIC CLUSTER(Non-covalent)

CUB.4: 16 residues within 4Å: Chain B: Q.240, F.271, G.272, V.275, A.346, V.384, A.385, Y.386, R.387, C.388, S.389, F.390, Y.568, G.569, E.763 Ligands: MCN.5 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:V.275, B:A.346, B:V.384, B:F.390, B:Y.568 Hydrogen bonds: B:Q.240, B:S.389, B:F.390, B:G.569 Water bridges: B:Q.528 Salt bridges: B:E.763 Metal complexes: B:C.388 CUB.9: 16 residues within 4Å: Chain E: Q.240, F.271, G.272, V.275, A.346, V.384, A.385, Y.386, R.387, C.388, S.389, F.390, Y.568, G.569, E.763 Ligands: MCN.10 11 PLIP interactions: 11 interactions with chain E, Hydrophobic interactions: E:V.275, E:A.346, E:V.384, E:F.390 Hydrogen bonds: E:Q.240, E:S.389, E:F.390, E:G.569 Water bridges: E:Q.528 Salt bridges: E:E.763 Metal complexes: E:C.388

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: CUB.4 26 PLIP interactions: 2 interactions with chain A, 24 interactions with chain B Hydrogen bonds: A:Q.101, A:C.102, B:G.270, B:F.271, B:T.535, B:T.535, B:R.571, 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 Hydrophobic interactions: B:T.573, B:V.761 Water bridges: B:R.387, B:R.387, B:Q.528, B:Y.536, B:Y.536 Salt bridges: B:H.532 MCN.10: 36 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, 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: CUB.9 26 PLIP interactions: 24 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:V.761 Hydrogen bonds: E:G.270, E:F.271, E:Q.530, E:T.535, E:R.571, 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, D:C.102 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: 31 residues within 4Å: Chain A: S.45, H.46 Chain C: R.29, P.30, L.31, A.32, G.33, G.34, H.35, S.36, L.37, A.74, L.100, I.101, A.102, I.106, G.110, T.111, G.114, N.115, A.117, N.118, N.123, D.124, I.161, L.166, L.167, K.185, G.191, D.192, Y.193 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:A.102, C:I.106, C:I.106 Hydrogen bonds: C:R.29, C:P.30, C:A.32, C:G.33, C:G.34, C:H.35, C:S.36, C:S.36, C:L.37, C:A.102, C:T.111, C:N.115, C:N.123, C:D.124, C:D.124, C:D.124, C:L.167, C:L.167, C:K.185 Water bridges: C:R.29, C:N.118 FAD.11: 33 residues within 4Å: Chain D: T.44, S.45, H.46 Chain F: R.29, P.30, L.31, A.32, G.33, G.34, H.35, S.36, L.37, L.54, A.74, L.100, I.101, A.102, I.106, G.110, T.111, G.114, N.115, A.117, N.118, N.123, D.124, I.161, L.166, L.167, K.185, G.191, D.192, Y.193 26 PLIP interactions: 26 interactions with chain F Hydrophobic interactions: F:A.102, F:I.106, F:I.106 Hydrogen bonds: F:R.29, F:P.30, F:A.32, F:G.33, F:G.34, F:H.35, F:S.36, F:S.36, F:L.37, F:A.102, F:T.111, F:N.115, F:N.123, F:D.124, F:D.124, F:L.167, F:L.167, F:K.185 Water bridges: F:R.29, F:T.111, F:N.118, F:N.118, 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

2002-12-18

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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