SMTL ID : 6he2.1

Crystal structure of an open conformation of 2-Hydroxyisobutyryl-CoA Ligase (HCL) in complex with 2-HIB-AMP and CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 14 residues within 4Å: Chain A: K.97, G.251, E.252, P.253, D.274, C.275, G.276, S.277, M.278, A.279, E.280, D.344, I.366 Ligands: 8LE.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.251, A:D.274, A:A.279, A:E.280, A:D.344 Water bridges: A:D.344, A:I.366, A:R.369 Salt bridges: A:K.97 AMP.4: 14 residues within 4Å: Chain B: K.97, G.251, E.252, P.253, D.274, C.275, G.276, S.277, M.278, A.279, E.280, D.344, I.366 Ligands: 8LE.5 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.251, B:D.274, B:A.279, B:E.280, B:D.344, B:R.369 Water bridges: B:K.97, B:S.342, B:I.366 Salt bridges: B:K.97

2 x 8LE: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] 2-methyl-2-oxidanyl-propanoate(Non-covalent)

8LE.2: 15 residues within 4Å: Chain A: S.250, G.251, E.252, P.253, D.274, C.275, G.276, S.277, M.278, A.279, E.280, F.284, D.344, I.366 Ligands: AMP.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.284, A:F.284 Hydrogen bonds: A:S.250, A:G.251, A:D.274, A:A.279, A:D.344 Water bridges: A:G.177, A:D.344, A:I.366, A:R.369 8LE.5: 15 residues within 4Å: Chain B: S.250, G.251, E.252, P.253, D.274, C.275, G.276, S.277, M.278, A.279, E.280, F.284, D.344, I.366 Ligands: AMP.4 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.284 Hydrogen bonds: B:S.250, B:G.251, B:D.274, B:A.279, B:D.344, B:R.369 Water bridges: B:G.177, B:S.342, B:I.366

2 x COA: COENZYME A(Non-covalent)

COA.3: 9 residues within 4Å: Chain A: G.198, A.199, P.200, G.201, M.202, S.203, S.223, Y.224, H.227 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.198, A:G.198, A:G.201, A:M.202, A:S.203, A:S.203, A:S.203, A:S.223 Water bridges: A:A.204, A:A.204, A:H.227 Salt bridges: A:H.227, A:H.227 pi-Stacking: A:Y.224 COA.6: 10 residues within 4Å: Chain B: Y.175, G.198, A.199, P.200, G.201, M.202, S.203, S.223, Y.224, H.227 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:G.198, B:G.198, B:G.201, B:M.202, B:S.203, B:S.203, B:S.223 Water bridges: B:A.204, B:A.204, B:Y.224, B:H.227 Salt bridges: B:H.227, B:H.227 pi-Stacking: B:Y.224, B:H.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zahn, M. et al., Structures of 2-Hydroxyisobutyric Acid-CoA Ligase Reveal Determinants of Substrate Specificity and Describe a Multi-Conformational Catalytic Cycle. J.Mol.Biol. (2019)

Release Date

2019-08-28

Peptides

2-hydroxyisobutyryl-CoA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

2-hydroxyisobutyryl-CoA synthetase

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