SMTL ID : 2z8y.2 (1 other biounit)

Xenon-bound structure of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase(CODH/ACS) from Moorella thermoacetica

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

hetero-2-2-mer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: C.68, F.70, C.71, A.73, G.74, C.76, G.88, I.89, C.90, R.100, M.221 Chain B: M.584 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.68, A:C.71, A:C.76, A:C.90 SF4.2: 10 residues within 4Å: Chain A: C.59, G.62, C.67, R.69, R.77 Chain B: C.59, I.61, G.62, C.67, R.69 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, Metal complexes: B:C.59, B:C.67, A:C.59, A:C.67 SF4.12: 11 residues within 4Å: Chain A: M.584 Chain B: C.68, F.70, C.71, A.73, G.74, C.76, G.88, C.90, R.100, M.221 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.68, B:C.71, B:C.76, B:C.90 SF4.24: 12 residues within 4Å: Chain C: I.146, C.506, V.507, L.508, C.509, C.518, G.526, L.527, C.528, V.531, C.595, C.597 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.506, C:C.509, C:C.518, C:C.528 SF4.30: 11 residues within 4Å: Chain D: C.506, L.508, C.509, C.518, G.526, L.527, C.528, V.531, C.595, C.597 Ligands: CU1.28 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.506, D:C.509, D:C.518, D:C.528

2 x XCC: FE(4)-NI(1)-S(4) CLUSTER(Covalent)(Non-covalent)

XCC.3: 10 residues within 4Å: Chain A: H.283, C.316, C.317, C.355, G.469, C.470, C.500, C.550, S.585, K.587 7 PLIP interactions: 7 interactions with chain A, Metal complexes: A:H.283, A:C.317, A:C.355, A:C.470, A:C.500, A:C.550, A:S.585 XCC.13: 10 residues within 4Å: Chain B: H.283, C.316, C.317, C.355, G.469, C.470, C.500, C.550, S.585, K.587 7 PLIP interactions: 7 interactions with chain B, Metal complexes: B:H.283, B:C.317, B:C.355, B:C.470, B:C.500, B:C.550, B:S.585

19 x XE: XENON(Non-covalent)

XE.4: 5 residues within 4Å: Chain A: C.468, A.580, G.592, W.595, T.602 Ligand excluded by PLIP XE.5: 4 residues within 4Å: Chain A: V.102, A.589, T.593, F.632 Ligand excluded by PLIP XE.6: 3 residues within 4Å: Chain A: I.106, A.234, L.620 Ligand excluded by PLIP XE.7: 2 residues within 4Å: Chain A: V.596, L.620 Ligand excluded by PLIP XE.8: 3 residues within 4Å: Chain A: I.623, V.627 Chain C: T.31 Ligand excluded by PLIP XE.9: 7 residues within 4Å: Chain A: L.287, T.374, I.386, Y.388, S.396, A.397, A.400 Ligand excluded by PLIP XE.14: 6 residues within 4Å: Chain B: C.468, A.580, G.592, W.595, T.602, H.603 Ligand excluded by PLIP XE.15: 5 residues within 4Å: Chain B: V.102, A.589, T.593, P.608, F.632 Ligand excluded by PLIP XE.16: 2 residues within 4Å: Chain B: I.106, L.620 Ligand excluded by PLIP XE.17: 2 residues within 4Å: Chain B: I.235, L.620 Ligand excluded by PLIP XE.18: 2 residues within 4Å: Chain B: I.623 Chain D: T.31 Ligand excluded by PLIP XE.19: 6 residues within 4Å: Chain B: L.287, T.374, Y.388, S.396, A.397, A.400 Ligand excluded by PLIP XE.25: 3 residues within 4Å: Chain C: T.213, I.215, V.261 Ligand excluded by PLIP XE.26: 2 residues within 4Å: Chain C: I.215, A.265 Ligand excluded by PLIP XE.27: 4 residues within 4Å: Chain C: V.149, F.229, C.509 Ligands: CU1.22 Ligand excluded by PLIP XE.31: 4 residues within 4Å: Chain D: F.212, T.213, I.215, V.261 Ligand excluded by PLIP XE.32: 2 residues within 4Å: Chain D: I.215, A.265 Ligand excluded by PLIP XE.33: 5 residues within 4Å: Chain D: M.148, E.156, M.182, Y.221, I.248 Ligand excluded by PLIP XE.34: 5 residues within 4Å: Chain D: V.149, F.229, C.509 Ligands: CU1.28, NI.29 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 5 residues within 4Å: Chain A: V.45, I.46, R.51, A.362, V.363 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.46, A:R.51, B:R.87 GOL.11: 9 residues within 4Å: Chain A: S.8, H.9, N.10, R.12, P.13, S.14, V.640, R.643, K.644 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.10, A:N.10, A:R.643, A:K.644 GOL.20: 4 residues within 4Å: Chain B: V.45, I.46, A.362, V.363 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.46 Water bridges: B:R.51 GOL.21: 7 residues within 4Å: Chain B: A.94, W.95, G.612, S.613, D.614, L.615 Chain D: H.27 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:S.613, B:D.614, B:L.615, D:H.27 Water bridges: B:G.612

2 x CU1: COPPER (I) ION(Non-covalent)

CU1.22: 6 residues within 4Å: Chain C: C.509, C.595, G.596, C.597 Ligands: NI.23, XE.27 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.509, C:C.595, C:C.597 CU1.28: 6 residues within 4Å: Chain D: C.509, C.595, C.597 Ligands: NI.29, SF4.30, XE.34 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.509, D:C.595, D:C.597

2 x NI: NICKEL (II) ION(Non-covalent)

NI.23: 6 residues within 4Å: Chain C: L.527, C.595, G.596, C.597, F.598 Ligands: CU1.22 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:C.595, C:C.597 NI.29: 6 residues within 4Å: Chain D: C.595, G.596, C.597, F.598 Ligands: CU1.28, XE.34 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:C.595, D:C.597

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Doukov, T.I. et al., Xenon in and at the End of the Tunnel of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase. Biochemistry (2008)

Release Date

2008-03-11

Peptides

Carbon monoxide dehydrogenase/acetyl CoA synthase subunit beta: AB
Carbon monoxide dehydrogenase/acetyl CoA synthase subunit alpha: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
O

D
P

Carbon monoxide dehydrogenase/acetyl CoA synthase subunit beta

Carbon monoxide dehydrogenase/acetyl CoA synthase subunit alpha

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