SMTL ID : 6ktq.1

Crystal structure of catalytic domain of homocitrate synthase from Sulfolobus acidocaldarius (SaHCS(dRAM)) in complex with alpha-ketoglutarate/Zn2+/CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: E.42, H.227, H.229 Ligands: AKG.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.42, A:H.227, A:H.229, H2O.6 ZN.10: 4 residues within 4Å: Chain B: E.42, H.227, H.229 Ligands: AKG.11 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.42, B:H.227, B:H.229, H2O.12

2 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.2: 13 residues within 4Å: Chain A: R.41, E.42, H.105, R.165, T.167, E.169, S.195, A.197, T.199, H.227, H.229, H.251 Ligands: ZN.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:T.167 Hydrogen bonds: A:R.41, A:R.41, A:T.167, A:E.169, A:S.195 Water bridges: A:Q.45 Salt bridges: A:R.41, A:H.105, A:R.165, A:H.227, A:H.227, A:H.229, A:H.251 AKG.11: 14 residues within 4Å: Chain B: R.41, E.42, H.105, R.165, T.167, E.169, S.195, A.197, T.199, H.227, H.229, H.251 Ligands: ZN.10, COA.12 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:T.167 Hydrogen bonds: B:R.41, B:R.41, B:E.169, B:S.195, B:S.195 Salt bridges: B:R.41, B:H.105, B:R.165, B:H.227, B:H.227, B:H.229, B:H.251

2 x COA: COENZYME A(Non-covalent)

COA.3: 10 residues within 4Å: Chain A: H.75, V.78, R.107, A.108, V.109, F.127, Y.128, K.138, H.139, E.169 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.78 Hydrogen bonds: A:Q.45, A:R.107, A:A.108, A:F.127, A:K.138 Water bridges: A:H.139 pi-Stacking: A:H.139 COA.12: 12 residues within 4Å: Chain B: Q.45, H.75, V.78, R.107, A.108, V.109, F.127, Y.128, K.138, H.139, E.169 Ligands: AKG.11 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.78 Hydrogen bonds: B:Q.45, B:R.107, B:A.108, B:F.127, B:K.138 Water bridges: B:H.75 pi-Stacking: B:H.139

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

SO4.4: 2 residues within 4Å: Chain A: N.385, R.387 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.385 Water bridges: A:N.385, A:N.385, A:R.387 Salt bridges: A:R.387 SO4.5: 2 residues within 4Å: Chain A: R.342, S.343 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.343 Water bridges: A:R.342, A:R.342 Salt bridges: A:R.342 SO4.7: 3 residues within 4Å: Chain A: L.13, R.16 Chain B: K.213 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Water bridges: B:R.209, B:K.213, A:R.16, A:R.16, A:R.16 Salt bridges: B:K.213, A:R.16 SO4.8: 4 residues within 4Å: Chain A: R.209, K.213 Chain B: R.209, K.213 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Water bridges: B:R.209 Salt bridges: B:R.209, B:K.213, A:R.209, A:K.213 SO4.9: 3 residues within 4Å: Chain A: K.213 Chain B: L.13, R.16 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Water bridges: B:R.16, B:R.16 Salt bridges: B:R.16, A:K.213 SO4.13: 2 residues within 4Å: Chain B: R.342, S.343 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.343, B:S.343 Salt bridges: B:R.342 SO4.14: 2 residues within 4Å: Chain B: T.369, D.370 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.370 Water bridges: B:T.369, B:S.371 SO4.15: 2 residues within 4Å: Chain B: R.387, R.390 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.387, B:R.390

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.6: 4 residues within 4Å: Chain A: Y.176, E.210, D.214 Chain B: R.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.210, A:D.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suzuki, T. et al., Involvement of subdomain II in the recognition of acetyl-CoA revealed by the crystal structure of homocitrate synthase from Sulfolobus acidocaldarius. Febs J. (2021)

Release Date

2020-09-02

Peptides

Homocitrate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Homocitrate synthase