SMTL ID : 6hdy.1

Crystal structure of 2-Hydroxyisobutyryl-CoA Ligase (HCL) in the postadenylation state in complex with S3-HB-AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x 3HL: (3S)-3-HYDROXYBUTANOIC ACID(Non-covalent)

3HL.1: 11 residues within 4Å: Chain A: Y.175, M.176, G.177, S.250, G.251, G.276, S.277, M.278, A.279, F.284 Ligands: 8LQ.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.175, A:M.176, A:A.279 Hydrogen bonds: A:Y.175, A:S.250, A:S.277 3HL.6: 11 residues within 4Å: Chain B: Y.175, M.176, G.177, S.250, G.251, G.276, S.277, M.278, A.279, F.284 Ligands: 8LQ.7 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.175, B:M.176, B:A.279 Hydrogen bonds: B:S.250, B:S.277

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

8LQ.2: 20 residues within 4Å: Chain A: Y.175, G.177, Y.219, 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, R.369, K.466 Ligands: 3HL.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.284 Hydrogen bonds: A:Y.175, A:Y.219, A:G.251, A:D.274, A:A.279, A:D.344, A:K.466 Water bridges: A:I.366, A:R.369, A:R.369, A:R.369 Salt bridges: A:K.466, A:K.466 8LQ.7: 20 residues within 4Å: Chain B: Y.175, G.177, Y.219, 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, R.369, K.466 Ligands: 3HL.6 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.284 Hydrogen bonds: B:Y.219, B:Y.219, B:G.251, B:D.274, B:A.279, B:D.344, B:K.466 Water bridges: B:I.366, B:R.369, B:R.369, B:R.369 Salt bridges: B:K.466, B:K.466

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

SO4.3: 5 residues within 4Å: Chain A: F.67, R.70, S.103, H.107, D.112 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.103 Salt bridges: A:R.70, A:H.107 SO4.4: 3 residues within 4Å: Chain A: E.352, P.354, R.361 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.295 Salt bridges: A:R.361 SO4.5: 6 residues within 4Å: Chain A: A.199, P.200, G.201, M.202, S.203, H.227 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.199, A:G.201, A:M.202, A:S.203, A:S.203 SO4.8: 5 residues within 4Å: Chain B: F.67, R.70, S.103, H.107, D.112 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.103 Salt bridges: B:R.70, B:H.107 SO4.9: 3 residues within 4Å: Chain B: E.352, P.354, R.361 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.361 Salt bridges: B:R.361 SO4.10: 6 residues within 4Å: Chain B: A.199, P.200, G.201, M.202, S.203, H.227 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.199, B:G.201, B:M.202, B:S.203, B:S.203

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
A

2-hydroxyisobutyryl-CoA synthetase

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