SMTL ID : 8uem.1

The CryoEM structure of the high affinity Carbon monoxide dehydrogenase from Mycobacterium smegmatis

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

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

CUN.1: 15 residues within 4Å: Chain A: Q.233, F.264, G.265, V.268, V.377, A.378, Y.379, A.380, C.381, S.382, T.554, Y.555, G.556, E.752 Ligands: MCN.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.233, A:G.556, A:E.752 Water bridges: A:F.264 Metal complexes: A:C.381 CUN.6: 15 residues within 4Å: Chain D: Q.233, F.264, G.265, V.268, V.377, A.378, Y.379, A.380, C.381, S.382, T.554, Y.555, G.556, E.752 Ligands: MCN.7 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.233, D:G.556, D:E.752 Water bridges: D:F.264 Metal complexes: D:C.381

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

MCN.2: 36 residues within 4Å: Chain A: G.262, G.263, F.264, G.265, A.380, Q.515, G.516, Q.517, G.518, H.519, T.522, T.554, Y.555, G.556, S.557, R.558, S.559, T.560, P.561, C.675, T.677, R.678, I.679, N.680, I.683, I.684, Q.687, A.747, K.748, G.749, I.750, G.751, E.752 Chain C: Q.97, C.135 Ligands: CUN.1 22 PLIP interactions: 20 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:T.560, A:I.750 Hydrogen bonds: A:G.263, A:F.264, A:Q.517, A:T.522, A:S.559, A:S.559, A:T.560, A:T.560, A:T.677, A:I.679, A:N.680, A:Q.687, A:K.748, A:I.750, A:G.751, C:Q.97 Water bridges: A:Q.515, A:T.522, C:Q.97 Salt bridges: A:H.519 MCN.7: 36 residues within 4Å: Chain D: G.262, G.263, F.264, G.265, A.380, Q.515, G.516, Q.517, G.518, H.519, T.522, T.554, Y.555, G.556, S.557, R.558, S.559, T.560, P.561, C.675, T.677, R.678, I.679, N.680, I.683, I.684, Q.687, A.747, K.748, G.749, I.750, G.751, E.752 Chain F: Q.97, C.135 Ligands: CUN.6 23 PLIP interactions: 21 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: D:T.560, D:I.750 Hydrogen bonds: D:G.263, D:F.264, D:Q.517, D:T.522, D:S.559, D:S.559, D:T.560, D:T.560, D:T.677, D:I.679, D:N.680, D:Q.687, D:K.748, D:I.750, D:G.751, F:Q.97 Water bridges: D:G.265, D:Q.515, D:T.522, F:Q.97 Salt bridges: D:H.519

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

FAD.3: 35 residues within 4Å: Chain B: R.30, I.31, V.32, A.33, G.34, G.35, H.36, S.37, L.38, I.55, A.76, H.80, V.102, I.103, A.104, V.108, G.112, T.113, G.115, G.116, S.117, C.119, Q.120, E.125, D.126, L.163, M.168, L.169, K.186, G.192, D.193, W.194 Chain C: T.41, S.42, N.43 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:A.104, B:V.108 Hydrogen bonds: B:R.30, B:I.31, B:I.31, B:A.33, B:G.34, B:G.35, B:H.36, B:S.37, B:L.38, B:H.80, B:A.104, B:T.113, B:G.116, B:D.126, B:D.126, B:L.127, B:L.169, B:L.169, B:K.186 Water bridges: B:A.195 pi-Stacking: B:W.194, B:W.194, B:W.194, B:W.194 FAD.8: 35 residues within 4Å: Chain E: R.30, I.31, V.32, A.33, G.34, G.35, H.36, S.37, L.38, I.55, A.76, H.80, V.102, I.103, A.104, V.108, G.112, T.113, G.115, G.116, S.117, C.119, Q.120, E.125, D.126, L.163, M.168, L.169, K.186, G.192, D.193, W.194 Chain F: T.41, S.42, N.43 27 PLIP interactions: 27 interactions with chain E Hydrophobic interactions: E:A.104, E:V.108, E:V.108 Hydrogen bonds: E:R.30, E:I.31, E:I.31, E:A.33, E:G.34, E:G.35, E:H.36, E:S.37, E:L.38, E:H.80, E:A.104, E:T.113, E:G.116, E:D.126, E:D.126, E:L.127, E:L.169, E:L.169, E:K.186 Water bridges: E:A.195 pi-Stacking: E:W.194, E:W.194, E:W.194, E:W.194

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

FES.4: 12 residues within 4Å: Chain B: M.1 Chain C: W.37, G.38, C.39, S.42, N.43, C.44, G.45, T.46, C.47, K.57, C.59 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.39, C:C.44, C:C.47, C:C.59 FES.5: 9 residues within 4Å: Chain A: M.210 Chain C: L.96, Q.97, C.98, G.99, C.101, C.133, R.134, C.135 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.98, C:C.101, C:C.133, C:C.135 FES.9: 11 residues within 4Å: Chain E: M.1 Chain F: W.37, G.38, C.39, S.42, N.43, C.44, G.45, C.47, K.57, C.59 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.39, F:C.44, F:C.47, F:C.59 FES.10: 10 residues within 4Å: Chain D: M.210 Chain F: L.96, Q.97, C.98, G.99, C.101, C.133, R.134, C.135, T.136 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.98, F:C.101, F:C.133, F:C.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gillett, D. et al., Structural basis for bacterial energy extraction from atmospheric hydrogen. To Be Published

Release Date

2024-10-16

Peptides

Carbon monoxide dehydrogenase (Large chain), CoxL: AD
Carbon monoxide dehydrogenase medium chain: BE
[2Fe-2S] binding domain protein: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

Carbon monoxide dehydrogenase (Large chain), CoxL

Carbon monoxide dehydrogenase medium chain

[2Fe-2S] binding domain protein