SMTL ID : 3git.7 (6 other biounits)

Crystal structure of a truncated acetyl-CoA synthase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-hexamer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: R.95, C.196, L.198, C.199, C.208, G.216, L.217, C.218, V.221, C.285, C.287 Ligands: ZN.2 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.196, A:C.199, A:C.208, A:C.218 SF4.10: 12 residues within 4Å: Chain B: R.95, C.196, L.198, C.199, C.208, G.216, L.217, C.218, V.221, C.285, C.287 Ligands: ZN.11 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.196, B:C.199, B:C.208, B:C.218 SF4.18: 12 residues within 4Å: Chain C: R.95, C.196, L.198, C.199, H.206, C.208, G.216, L.217, C.218, V.221, C.287 Ligands: ZN.19 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.196, C:C.199, C:C.208, C:C.218 SF4.27: 12 residues within 4Å: Chain D: R.95, C.196, L.198, C.199, C.208, G.216, L.217, C.218, V.221, C.285, C.287 Ligands: ZN.28 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.196, D:C.199, D:C.208, D:C.218 SF4.34: 12 residues within 4Å: Chain E: R.95, C.196, L.198, C.199, C.208, G.216, L.217, C.218, V.221, C.285, C.287 Ligands: ZN.35 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.196, E:C.199, E:C.208, E:C.218 SF4.42: 11 residues within 4Å: Chain F: R.95, C.196, L.198, C.199, C.208, G.216, L.217, C.218, V.221, C.287 Ligands: ZN.43 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.196, F:C.199, F:C.208, F:C.218

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.199, C.285, C.287 Ligands: SF4.1, H2S.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.199, A:C.285, A:C.287 ZN.11: 6 residues within 4Å: Chain B: C.199, C.285, G.286, C.287 Ligands: SF4.10, H2S.12 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.199, B:C.285, B:C.287 ZN.19: 6 residues within 4Å: Chain C: C.199, C.285, G.286, C.287 Ligands: SF4.18, H2S.20 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.199, C:C.285, C:C.287 ZN.28: 6 residues within 4Å: Chain D: C.199, C.285, G.286, C.287 Ligands: SF4.27, H2S.29 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.199, D:C.285, D:C.287 ZN.35: 6 residues within 4Å: Chain E: C.199, C.285, G.286, C.287 Ligands: SF4.34, H2S.36 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.199, E:C.285, E:C.287 ZN.43: 6 residues within 4Å: Chain F: C.199, C.285, G.286, C.287 Ligands: SF4.42, H2S.44 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.199, F:C.285, F:C.287

6 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.3: 6 residues within 4Å: Chain A: C.199, F.202, C.285, G.286, C.287 Ligands: ZN.2 No protein-ligand interaction detected (PLIP) H2S.12: 6 residues within 4Å: Chain B: C.199, F.202, C.285, G.286, C.287 Ligands: ZN.11 No protein-ligand interaction detected (PLIP) H2S.20: 6 residues within 4Å: Chain C: C.199, F.202, C.285, G.286, C.287 Ligands: ZN.19 No protein-ligand interaction detected (PLIP) H2S.29: 6 residues within 4Å: Chain D: C.199, F.202, C.285, G.286, C.287 Ligands: ZN.28 No protein-ligand interaction detected (PLIP) H2S.36: 6 residues within 4Å: Chain E: C.199, F.202, C.285, G.286, C.287 Ligands: ZN.35 No protein-ligand interaction detected (PLIP) H2S.44: 6 residues within 4Å: Chain F: C.199, F.202, C.285, G.286, C.287 Ligands: ZN.43 No protein-ligand interaction detected (PLIP)

24 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: P.67, E.68 Chain E: K.25, K.71 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: E.244, G.245, E.246 Ligand excluded by PLIP SO4.7: 5 residues within 4Å: Chain A: I.23, R.24, K.25, R.119 Ligands: GOL.6 Ligand excluded by PLIP SO4.8: 2 residues within 4Å: Chain A: R.44, Y.167 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: K.25, K.71 Chain F: P.67, E.68 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain B: E.244, G.245, E.246 Ligand excluded by PLIP SO4.15: 5 residues within 4Å: Chain B: I.23, R.24, K.25, R.119 Ligands: GOL.14 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain B: R.44, Y.167 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain B: K.25, K.71 Chain C: P.67, E.68 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain C: E.244, G.245, E.246 Ligand excluded by PLIP SO4.23: 5 residues within 4Å: Chain C: I.23, R.24, K.25, R.119 Ligands: GOL.22 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain C: R.44, Y.167 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain C: K.25, K.71 Chain D: P.67, E.68 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain B: P.67, E.68 Chain D: K.25, K.71 Ligand excluded by PLIP SO4.30: 3 residues within 4Å: Chain D: E.244, G.245, E.246 Ligand excluded by PLIP SO4.32: 5 residues within 4Å: Chain D: I.23, R.24, K.25, R.119 Ligands: GOL.31 Ligand excluded by PLIP SO4.33: 2 residues within 4Å: Chain D: R.44, Y.167 Ligand excluded by PLIP SO4.37: 3 residues within 4Å: Chain E: E.244, G.245, E.246 Ligand excluded by PLIP SO4.39: 5 residues within 4Å: Chain E: I.23, R.24, K.25, R.119 Ligands: GOL.38 Ligand excluded by PLIP SO4.40: 2 residues within 4Å: Chain E: R.44, Y.167 Ligand excluded by PLIP SO4.41: 4 residues within 4Å: Chain E: P.67, E.68 Chain F: K.25, K.71 Ligand excluded by PLIP SO4.45: 3 residues within 4Å: Chain F: E.244, G.245, E.246 Ligand excluded by PLIP SO4.47: 5 residues within 4Å: Chain F: I.23, R.24, K.25, R.119 Ligands: GOL.46 Ligand excluded by PLIP SO4.48: 2 residues within 4Å: Chain F: R.44, Y.167 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: S.22, I.23, W.108, W.117, R.119 Ligands: SO4.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.23 Water bridges: A:S.22 GOL.14: 6 residues within 4Å: Chain B: S.22, I.23, W.108, W.117, R.119 Ligands: SO4.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.23 Water bridges: B:W.108 GOL.22: 6 residues within 4Å: Chain C: S.22, I.23, W.108, W.117, R.119 Ligands: SO4.23 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.23 GOL.31: 6 residues within 4Å: Chain D: S.22, I.23, W.108, W.117, R.119 Ligands: SO4.32 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:I.23 GOL.38: 6 residues within 4Å: Chain E: S.22, I.23, W.108, W.117, R.119 Ligands: SO4.39 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:I.23 GOL.46: 6 residues within 4Å: Chain F: S.22, I.23, W.108, W.117, R.119 Ligands: SO4.47 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:I.23, F:I.23 Water bridges: F:W.108

Links

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Citation

Volbeda, A. et al., Novel domain arrangement in the crystal structure of a truncated acetyl-CoA synthase from Moorella thermoacetica. Biochemistry (2009)

Release Date

2009-10-06

Peptides

Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha

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