SMTL ID : 8cja.1

A225L/F231A variant of the CODH/ACS complex of C. hydrogenoformans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-4-mer

Ligands

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

MPD.1: 8 residues within 4Å: Chain A: V.226, T.229, A.230, L.233, I.614, V.622, Y.623 Chain E: Y.41 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain A Hydrophobic interactions: E:Y.41, A:V.226, A:A.230, A:V.622 Hydrogen bonds: A:Y.623 MPD.2: 11 residues within 4Å: Chain A: V.100, I.104, T.229, A.232, L.233, T.588, V.591, F.611, I.614, T.615, F.627 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.104, A:T.229, A:A.232, A:T.588, A:F.611, A:I.614, A:F.627 MPD.12: 8 residues within 4Å: Chain C: V.226, T.229, A.230, L.233, I.614, V.622, Y.623 Chain F: Y.41 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:V.226, C:A.230, C:V.622, F:Y.41 MPD.13: 11 residues within 4Å: Chain C: V.100, I.104, T.229, A.232, L.233, T.588, V.591, F.611, I.614, T.615, F.627 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:I.104, C:T.229, C:A.232, C:T.588, C:F.611, C:I.614, C:F.627

2 x RQM: Fe(3)-Ni(1)-S(4) cluster(Covalent)

RQM.3: 15 residues within 4Å: Chain A: H.281, C.314, C.315, F.332, C.353, G.465, C.466, G.495, C.496, C.545, M.579, S.580, K.582 Ligands: OH.5, OH.6 10 PLIP interactions: 6 interactions with chain A, 4 Ligand-Ligand interactions Metal complexes: A:H.281, A:C.315, A:C.353, A:C.466, A:C.496, A:C.545, OH.5, OH.5, OH.6, OH.6 RQM.14: 15 residues within 4Å: Chain C: H.281, C.314, C.315, F.332, C.353, G.465, C.466, G.495, C.496, C.545, M.579, S.580, K.582 Ligands: OH.16, OH.17 6 PLIP interactions: 6 interactions with chain C, Metal complexes: C:H.281, C:C.315, C:C.353, C:C.466, C:C.496, C:C.545

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

SF4.4: 11 residues within 4Å: Chain A: C.67, F.69, C.70, G.73, C.75, G.86, I.87, C.88, A.90, R.98, I.219 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.67, A:C.70, A:C.75, A:C.88 SF4.7: 9 residues within 4Å: Chain A: C.58, F.60, G.61, C.66, R.76 Chain C: C.58, C.66, R.68 Ligands: SF4.18 2 PLIP interactions: 2 interactions with chain A, Metal complexes: A:C.58, A:C.66 SF4.10: 12 residues within 4Å: Chain B: I.152, C.512, L.514, C.515, C.524, G.532, L.533, C.534, I.537, C.601, C.603 Ligands: NI.11 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.512, B:C.515, B:C.524, B:C.534 SF4.15: 11 residues within 4Å: Chain C: C.67, F.69, C.70, G.73, C.75, G.86, I.87, C.88, A.90, R.98, I.219 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.67, C:C.70, C:C.75, C:C.88 SF4.18: 9 residues within 4Å: Chain A: C.58, C.66, R.68 Chain C: C.58, F.60, G.61, C.66, R.76 Ligands: SF4.7 2 PLIP interactions: 2 interactions with chain C, Metal complexes: C:C.58, C:C.66 SF4.21: 12 residues within 4Å: Chain D: I.152, C.512, L.514, C.515, C.524, G.532, L.533, C.534, I.537, C.601, C.603 Ligands: NI.22 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.512, D:C.515, D:C.524, D:C.534 SF4.25: 12 residues within 4Å: Chain E: I.152, C.512, L.514, C.515, C.524, G.532, L.533, C.534, I.537, C.601, C.603 Ligands: NI.26 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.512, E:C.515, E:C.524, E:C.534 SF4.29: 12 residues within 4Å: Chain F: I.152, C.512, L.514, C.515, C.524, G.532, L.533, C.534, I.537, C.601, C.603 Ligands: NI.30 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.512, F:C.515, F:C.524, F:C.534

4 x OH: HYDROXIDE ION(Non-covalent)

OH.5: 4 residues within 4Å: Chain A: G.465, C.466, C.545 Ligands: RQM.3 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.548 OH.6: 5 residues within 4Å: Chain A: H.281, C.315, C.545, K.582 Ligands: RQM.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.111 Water bridges: A:V.546 OH.16: 4 residues within 4Å: Chain C: G.465, C.466, C.545 Ligands: RQM.14 1 PLIP interactions: 1 interactions with chain C Water bridges: C:N.548 OH.17: 5 residues within 4Å: Chain C: H.281, C.315, C.545, K.582 Ligands: RQM.14 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.582 Water bridges: C:V.546

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

ACT.8: 10 residues within 4Å: Chain B: G.151, I.152, V.155, F.235, C.515, F.518, C.601, C.603 Ligands: NI.9, NI.11 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.155, B:F.235, B:F.518 ACT.19: 10 residues within 4Å: Chain D: G.151, I.152, V.155, F.235, C.515, F.518, C.601, C.603 Ligands: NI.20, NI.22 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:V.155, D:F.235, D:F.518 ACT.23: 10 residues within 4Å: Chain E: G.151, I.152, V.155, F.235, C.515, F.518, C.601, C.603 Ligands: NI.24, NI.26 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:V.155, E:F.235, E:F.518 ACT.27: 10 residues within 4Å: Chain F: G.151, I.152, V.155, F.235, C.515, F.518, C.601, C.603 Ligands: NI.28, NI.30 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:V.155, F:F.235, F:F.518

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

NI.9: 7 residues within 4Å: Chain B: L.533, C.601, G.602, C.603, F.604 Ligands: ACT.8, NI.11 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.601, B:C.603 NI.11: 6 residues within 4Å: Chain B: C.515, C.601, C.603 Ligands: ACT.8, NI.9, SF4.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:C.515, B:C.601, B:C.603, ACT.8 NI.20: 7 residues within 4Å: Chain D: L.533, C.601, G.602, C.603, F.604 Ligands: ACT.19, NI.22 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:C.601, D:C.603 NI.22: 6 residues within 4Å: Chain D: C.515, C.601, C.603 Ligands: ACT.19, NI.20, SF4.21 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:C.515, D:C.601, D:C.603, ACT.19 NI.24: 7 residues within 4Å: Chain E: L.533, C.601, G.602, C.603, F.604 Ligands: ACT.23, NI.26 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:C.601, E:C.603 NI.26: 6 residues within 4Å: Chain E: C.515, C.601, C.603 Ligands: ACT.23, NI.24, SF4.25 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Ligand interactions Metal complexes: E:C.515, E:C.601, E:C.603, ACT.23 NI.28: 7 residues within 4Å: Chain F: L.533, C.601, G.602, C.603, F.604 Ligands: ACT.27, NI.30 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:C.601, F:C.603 NI.30: 6 residues within 4Å: Chain F: C.515, C.601, C.603 Ligands: ACT.27, NI.28, SF4.29 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: F:C.515, F:C.601, F:C.603, ACT.27

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: AC
CO-methylating acetyl-CoA synthase: BDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

E
B

F
B

Carbon monoxide dehydrogenase

CO-methylating acetyl-CoA synthase

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