SMTL ID : 7tsj.1

Xenon-bound structure of carbon monoxide dehydrogenase (CODH) from Desulfovibrio vulgaris

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: C.59, N.61, C.62, M.64, G.65, C.67, G.80, V.81, C.82, I.89, R.92, M.211 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.59, A:C.62, A:C.67, A:C.82 SF4.16: 12 residues within 4Å: Chain B: C.59, N.61, C.62, M.64, G.65, C.67, G.80, V.81, C.82, I.89, R.92, M.211 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.59, B:C.62, B:C.67, B:C.82

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

FES.2: 7 residues within 4Å: Chain A: C.50, F.52, C.53, T.58, R.68 Chain B: C.53 Ligands: FES.17 2 PLIP interactions: 2 interactions with chain A, Metal complexes: A:C.50, A:C.53 FES.17: 7 residues within 4Å: Chain A: C.53 Chain B: C.50, F.52, C.53, T.58, R.68 Ligands: FES.2 2 PLIP interactions: 2 interactions with chain B, Metal complexes: B:C.50, B:C.53

2 x CUV: Fe(4)-Ni(1)-S(4) cluster, oxidized(Non-covalent)

CUV.3: 15 residues within 4Å: Chain A: H.274, C.309, C.310, N.313, H.327, C.348, G.455, C.456, G.485, C.486, C.527, Y.561, S.562, K.564, A.565 8 PLIP interactions: 8 interactions with chain A, Metal complexes: A:H.274, A:C.309, A:C.310, A:C.310, A:C.348, A:C.456, A:C.486, A:C.527 CUV.18: 15 residues within 4Å: Chain B: H.274, C.309, C.310, N.313, H.327, C.348, G.455, C.456, G.485, C.486, C.527, Y.561, S.562, K.564, A.565 8 PLIP interactions: 8 interactions with chain B, Metal complexes: B:H.274, B:C.309, B:C.310, B:C.310, B:C.348, B:C.456, B:C.486, B:C.527

24 x XE: XENON(Non-covalent)(Non-functional Binders)

XE.4: 4 residues within 4Å: Chain A: F.94, A.566, L.581, F.609 Ligand excluded by PLIP XE.5: 4 residues within 4Å: Chain A: L.581, P.585, A.597, F.609 Ligand excluded by PLIP XE.6: 2 residues within 4Å: Chain A: L.221, A.597 Ligand excluded by PLIP XE.7: 3 residues within 4Å: Chain A: L.221, V.222, M.596 Ligand excluded by PLIP XE.8: 4 residues within 4Å: Chain A: V.454, S.557, A.569, T.579 Ligand excluded by PLIP XE.9: 5 residues within 4Å: Chain A: F.450, G.452, I.533, V.553, G.554 Ligand excluded by PLIP XE.10: 2 residues within 4Å: Chain A: L.536, L.540 Ligand excluded by PLIP XE.11: 1 residues within 4Å: Chain A: L.544 Ligand excluded by PLIP XE.12: 3 residues within 4Å: Chain A: L.438, F.450, L.536 Ligand excluded by PLIP XE.13: 4 residues within 4Å: Chain A: L.438, M.480, L.516 Ligands: XE.14 Ligand excluded by PLIP XE.14: 3 residues within 4Å: Chain A: L.516, L.522 Ligands: XE.13 Ligand excluded by PLIP XE.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP XE.19: 4 residues within 4Å: Chain B: F.94, A.566, L.581, F.609 Ligand excluded by PLIP XE.20: 4 residues within 4Å: Chain B: L.581, P.585, A.597, F.609 Ligand excluded by PLIP XE.21: 2 residues within 4Å: Chain B: L.221, A.597 Ligand excluded by PLIP XE.22: 3 residues within 4Å: Chain B: L.221, V.222, M.596 Ligand excluded by PLIP XE.23: 4 residues within 4Å: Chain B: V.454, S.557, A.569, T.579 Ligand excluded by PLIP XE.24: 5 residues within 4Å: Chain B: F.450, G.452, I.533, V.553, G.554 Ligand excluded by PLIP XE.25: 2 residues within 4Å: Chain B: L.536, L.540 Ligand excluded by PLIP XE.26: 1 residues within 4Å: Chain B: L.544 Ligand excluded by PLIP XE.27: 3 residues within 4Å: Chain B: L.438, F.450, L.536 Ligand excluded by PLIP XE.28: 4 residues within 4Å: Chain B: L.438, M.480, L.516 Ligands: XE.29 Ligand excluded by PLIP XE.29: 3 residues within 4Å: Chain B: L.516, L.522 Ligands: XE.28 Ligand excluded by PLIP XE.30: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Biester, A. et al., Visualizing the gas channel of a monofunctional carbon monoxide dehydrogenase. J.Inorg.Biochem. (2022)

Release Date

2022-05-04

Peptides

Carbon monoxide dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Carbon monoxide dehydrogenase

Related Entries With Identical Sequence