SMTL ID : 8cjc.1

F515A variant of the CODH/ACS complex of C. hydrogenoformans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.22 Å

Oligo State

hetero-4-4-mer

Ligands

4 x RQM: Fe(3)-Ni(1)-S(4) cluster(Non-covalent)

RQM.1: 14 residues within 4Å: Chain A: H.288, C.321, C.322, F.339, C.360, G.472, C.473, C.503, C.552, M.586, S.587, K.589 Ligands: OH.4, OH.5 9 PLIP interactions: 6 interactions with chain A, 3 Ligand-Ligand interactions Metal complexes: A:H.288, A:C.322, A:C.360, A:C.473, A:C.503, A:C.552, OH.4, OH.5, OH.5 RQM.14: 14 residues within 4Å: Chain C: H.288, C.321, C.322, F.339, C.360, G.472, C.473, C.503, C.552, M.586, S.587, K.589 Ligands: OH.17, OH.18 6 PLIP interactions: 6 interactions with chain C, Metal complexes: C:H.288, C:C.322, C:C.360, C:C.473, C:C.503, C:C.552 RQM.27: 14 residues within 4Å: Chain E: H.288, C.321, C.322, F.339, C.360, G.472, C.473, C.503, C.552, M.586, S.587, K.589 Ligands: OH.30, OH.31 7 PLIP interactions: 6 interactions with chain E, 1 Ligand-Ligand interactions Metal complexes: E:H.288, E:C.322, E:C.360, E:C.473, E:C.503, E:C.552, OH.30 RQM.40: 14 residues within 4Å: Chain G: H.288, C.321, C.322, F.339, C.360, G.472, C.473, C.503, C.552, M.586, S.587, K.589 Ligands: OH.43, OH.44 9 PLIP interactions: 6 interactions with chain G, 3 Ligand-Ligand interactions Metal complexes: G:H.288, G:C.322, G:C.360, G:C.473, G:C.503, G:C.552, OH.43, OH.44, OH.44

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

SF4.2: 9 residues within 4Å: Chain A: C.65, F.67, G.68, C.73, R.83 Chain C: C.65, C.73, R.75 Ligands: SF4.15 2 PLIP interactions: 2 interactions with chain A, Metal complexes: A:C.65, A:C.73 SF4.3: 12 residues within 4Å: Chain A: C.74, R.75, F.76, C.77, G.80, C.82, G.93, I.94, C.95, A.97, R.105, I.226 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.74, A:C.77, A:C.82, A:C.95 SF4.9: 11 residues within 4Å: Chain B: I.145, C.505, L.507, C.508, C.517, G.525, L.526, C.527, I.530, C.596 Ligands: NI.10 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.505, B:C.508, B:C.517, B:C.527 SF4.15: 9 residues within 4Å: Chain A: C.65, C.73, R.75 Chain C: C.65, F.67, G.68, C.73, R.83 Ligands: SF4.2 2 PLIP interactions: 2 interactions with chain C, Metal complexes: C:C.65, C:C.73 SF4.16: 12 residues within 4Å: Chain C: C.74, R.75, F.76, C.77, G.80, C.82, G.93, I.94, C.95, A.97, R.105, I.226 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.74, C:C.77, C:C.82, C:C.95 SF4.22: 11 residues within 4Å: Chain D: I.145, C.505, L.507, C.508, C.517, G.525, L.526, C.527, I.530, C.596 Ligands: NI.23 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.505, D:C.508, D:C.517, D:C.527 SF4.28: 5 residues within 4Å: Chain E: C.65, F.67, G.68, C.73, R.83 2 PLIP interactions: 2 interactions with chain E, Metal complexes: E:C.65, E:C.73 SF4.29: 12 residues within 4Å: Chain E: C.74, R.75, F.76, C.77, G.80, C.82, G.93, I.94, C.95, A.97, R.105, I.226 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.74, E:C.77, E:C.82, E:C.95 SF4.35: 11 residues within 4Å: Chain F: I.145, C.505, L.507, C.508, C.517, G.525, L.526, C.527, I.530, C.596 Ligands: NI.36 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.505, F:C.508, F:C.517, F:C.527 SF4.41: 5 residues within 4Å: Chain G: C.65, F.67, G.68, C.73, R.83 2 PLIP interactions: 2 interactions with chain G, Metal complexes: G:C.65, G:C.73 SF4.42: 12 residues within 4Å: Chain G: C.74, R.75, F.76, C.77, G.80, C.82, G.93, I.94, C.95, A.97, R.105, I.226 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.74, G:C.77, G:C.82, G:C.95 SF4.48: 11 residues within 4Å: Chain H: I.145, C.505, L.507, C.508, C.517, G.525, L.526, C.527, I.530, C.596 Ligands: NI.49 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.505, H:C.508, H:C.517, H:C.527

8 x OH: HYDROXIDE ION(Non-covalent)

OH.4: 3 residues within 4Å: Chain A: C.552, I.593 Ligands: RQM.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.555 OH.5: 5 residues within 4Å: Chain A: H.288, C.322, C.552, K.589 Ligands: RQM.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.553 OH.17: 3 residues within 4Å: Chain C: C.552, I.593 Ligands: RQM.14 1 PLIP interactions: 1 interactions with chain C Water bridges: C:N.555 OH.18: 5 residues within 4Å: Chain C: H.288, C.322, C.552, K.589 Ligands: RQM.14 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.589 Water bridges: C:V.553 OH.30: 3 residues within 4Å: Chain E: C.552, I.593 Ligands: RQM.27 1 PLIP interactions: 1 interactions with chain E Water bridges: E:N.555 OH.31: 5 residues within 4Å: Chain E: H.288, C.322, C.552, K.589 Ligands: RQM.27 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:H.288 Water bridges: E:V.553 OH.43: 3 residues within 4Å: Chain G: C.552, I.593 Ligands: RQM.40 1 PLIP interactions: 1 interactions with chain G Water bridges: G:N.555 OH.44: 5 residues within 4Å: Chain G: H.288, C.322, C.552, K.589 Ligands: RQM.40 1 PLIP interactions: 1 interactions with chain G Water bridges: G:V.553

12 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6: 3 residues within 4Å: Chain A: P.266, V.268, Q.542 No protein-ligand interaction detected (PLIP) MPD.7: 6 residues within 4Å: Chain A: T.143, F.261, G.262, T.263, R.330, R.331 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.143, A:R.330 MPD.13: 4 residues within 4Å: Chain B: E.568, Y.571, E.579, R.580 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.568, B:Y.571, B:Y.571 Hydrogen bonds: B:E.579 MPD.19: 3 residues within 4Å: Chain C: P.266, V.268, Q.542 No protein-ligand interaction detected (PLIP) MPD.20: 6 residues within 4Å: Chain C: T.143, F.261, G.262, T.263, R.330, R.331 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:T.143, C:R.330 MPD.26: 4 residues within 4Å: Chain D: E.568, Y.571, E.579, R.580 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:E.568, D:Y.571, D:Y.571 Hydrogen bonds: D:E.579 MPD.32: 3 residues within 4Å: Chain E: P.266, V.268, Q.542 No protein-ligand interaction detected (PLIP) MPD.33: 6 residues within 4Å: Chain E: T.143, F.261, G.262, T.263, R.330, R.331 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:T.143, E:R.330 MPD.39: 4 residues within 4Å: Chain F: E.568, Y.571, E.579, R.580 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:E.568, F:Y.571, F:Y.571 Hydrogen bonds: F:E.579 MPD.45: 3 residues within 4Å: Chain G: P.266, V.268, Q.542 No protein-ligand interaction detected (PLIP) MPD.46: 6 residues within 4Å: Chain G: T.143, F.261, G.262, T.263, R.330, R.331 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:T.143, G:R.330 MPD.52: 4 residues within 4Å: Chain H: E.568, Y.571, E.579, R.580 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:E.568, H:Y.571, H:Y.571 Hydrogen bonds: H:E.579

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

NI.8: 6 residues within 4Å: Chain B: L.526, C.594, G.595, C.596, F.597 Ligands: NI.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.594, B:C.596 NI.10: 7 residues within 4Å: Chain B: I.145, C.508, C.594, C.596 Ligands: NI.8, SF4.9, ACT.11 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:C.508, B:C.594, B:C.596, ACT.11 NI.21: 6 residues within 4Å: Chain D: L.526, C.594, G.595, C.596, F.597 Ligands: NI.23 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:C.594, D:C.596 NI.23: 7 residues within 4Å: Chain D: I.145, C.508, C.594, C.596 Ligands: NI.21, SF4.22, ACT.24 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:C.508, D:C.594, D:C.596, ACT.24 NI.34: 6 residues within 4Å: Chain F: L.526, C.594, G.595, C.596, F.597 Ligands: NI.36 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:C.594, F:C.596 NI.36: 7 residues within 4Å: Chain F: I.145, C.508, C.594, C.596 Ligands: NI.34, SF4.35, ACT.37 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: F:C.508, F:C.594, F:C.596, ACT.37 NI.47: 6 residues within 4Å: Chain H: L.526, C.594, G.595, C.596, F.597 Ligands: NI.49 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:C.594, H:C.596 NI.49: 7 residues within 4Å: Chain H: I.145, C.508, C.594, C.596 Ligands: NI.47, SF4.48, ACT.50 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Ligand interactions Metal complexes: H:C.508, H:C.594, H:C.596, ACT.50

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.11: 8 residues within 4Å: Chain B: G.144, I.145, F.228, C.508, A.511, C.594, C.596 Ligands: NI.10 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.228, B:A.511 ACT.24: 8 residues within 4Å: Chain D: G.144, I.145, F.228, C.508, A.511, C.594, C.596 Ligands: NI.23 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.228, D:A.511 ACT.37: 8 residues within 4Å: Chain F: G.144, I.145, F.228, C.508, A.511, C.594, C.596 Ligands: NI.36 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:F.228, F:A.511 ACT.50: 8 residues within 4Å: Chain H: G.144, I.145, F.228, C.508, A.511, C.594, C.596 Ligands: NI.49 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:F.228, H:A.511

4 x NA: SODIUM ION(Non-functional Binders)

NA.12: 5 residues within 4Å: Chain B: F.327, E.330, N.411, G.413, F.416 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.411, B:F.416 Water bridges: B:E.330 NA.25: 5 residues within 4Å: Chain D: F.327, E.330, N.411, G.413, F.416 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.330, D:E.330, D:F.416 Water bridges: D:E.330 NA.38: 5 residues within 4Å: Chain F: F.327, E.330, N.411, G.413, F.416 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:G.413, F:F.416 Water bridges: F:E.330 NA.51: 5 residues within 4Å: Chain H: F.327, E.330, N.411, G.413, F.416 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:E.330, H:E.330, H:F.416 Water bridges: H:E.330

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruickoldt, J. et al., A225L variant of the CODH/ACS complex of C. hydrogenoformans. To Be Published

Release Date

2024-02-21

Peptides

Carbon monoxide dehydrogenase: ACEG
CO-methylating acetyl-CoA synthase: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

G
A

B
B

D
B

F
B

H
B

Carbon monoxide dehydrogenase

CO-methylating acetyl-CoA synthase