SMTL ID : 7wtd.1

Cryo-EM structure of human pyruvate carboxylase with acetyl-CoA in the intermediate state 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 13 residues within 4Å: Chain C: K.194, G.199, G.200, M.204, E.236, K.237, F.238, I.239, P.242, Q.268, H.271, K.273, E.324 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:K.194, C:K.237, C:I.239, C:Q.268, C:Q.268, C:H.271, C:E.324 Salt bridges: C:K.194, C:K.273 ATP.4: 15 residues within 4Å: Chain D: K.152, K.194, G.199, G.200, G.201, M.204, E.236, K.237, F.238, I.239, H.244, Q.268, H.271, I.323, E.324 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:K.194, D:G.199, D:G.200, D:E.236, D:I.239, D:Q.268, D:Q.268 Salt bridges: D:K.152, D:K.194

2 x COA: COENZYME A(Covalent)

COA.2: 19 residues within 4Å: Chain C: R.398, R.445, A.448, R.451, R.453, Q.494, R.496, A.497, Q.498, G.1055, K.1056, L.1080, R.1085 Chain D: T.57, Q.78, K.79, A.80, D.81, E.82 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:R.451, C:R.453, C:Q.494, C:R.496, C:K.1056, D:T.57, D:Q.78 Salt bridges: C:R.398, C:R.451, C:R.453, C:R.496, C:R.496, C:R.1085 COA.3: 25 residues within 4Å: Chain C: F.53, R.54, T.57, R.77, Q.78, K.79, A.80, D.81, E.82, A.83 Chain D: R.398, R.445, A.448, R.451, R.453, A.493, Q.494, R.496, A.497, Q.498, G.1055, K.1056, T.1057, L.1058, R.1085 18 PLIP interactions: 14 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:R.451, D:R.451, D:Q.494, D:Q.494, D:R.496, D:A.497, D:R.1085, C:Q.78, C:D.81, C:D.81, C:E.82 Salt bridges: D:R.398, D:R.451, D:R.451, D:R.453, D:R.453, D:R.453, D:R.496

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chai, P. et al., Mechanistic insight into allosteric activation of human pyruvate carboxylase by acetyl-CoA. Mol.Cell (2022)

Release Date

2022-11-09

Peptides

Pyruvate carboxylase, mitochondrial: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate carboxylase, mitochondrial

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