SMTL ID : 8e4y.1

Cryo-EM structure of human glycerol-3-phosphate acyltransferase 1 (GPAT1) in complex with 2-oxohexadecyl-CoA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.40 Å

Oligo State

monomer

Ligands

1 x UKL: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methyl (3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-{[3-oxo-3-({2-[(2-oxohexadecyl)sulfanyl]ethyl}amino)propyl]amino}butyl dihydrogen diphosphate (non-preferred name)(Non-covalent)

UKL.1: 26 residues within 4Å: Chain A: G.129, L.132, Y.175, L.176, T.179, F.183, I.192, A.193, S.194, L.198, L.210, R.216, R.217, R.218, L.219, K.227, R.232, F.252, G.255, R.267, A.268, G.269, L.270, S.272, R.401, I.404 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:L.132, A:Y.175, A:Y.175, A:L.176, A:T.179, A:F.183, A:I.192, A:I.192, A:L.210, A:L.219 Hydrogen bonds: A:Y.175, A:R.218, A:R.232, A:G.269, A:S.272, A:R.401, A:R.401, A:A.405 Salt bridges: A:R.217, A:K.227, A:R.232, A:R.267, A:R.401 pi-Cation interactions: A:R.401, A:R.401

1 x NKO: (2R)-2-hydroxy-3-(phosphonooxy)propyl hexadecanoate(Non-covalent)

NKO.2: 7 residues within 4Å: Chain A: L.176, F.203, E.300, H.302, Y.303, G.305, M.327 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.176, A:F.203 Hydrogen bonds: A:H.302, A:H.302, A:G.305 Salt bridges: A:H.302

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johnson, Z.L. et al., Structural basis of the acyl-transfer mechanism of human GPAT1. Nat.Struct.Mol.Biol. (2023)

Release Date

2022-12-21

Peptides

Glycerol-3-phosphate acyltransferase 1, mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glycerol-3-phosphate acyltransferase 1, mitochondrial

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