SMTL ID : 7wtc.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x BTI: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL(Covalent)

BTI.1: 11 residues within 4Å: Chain A: K.1144 Chain C: A.610, D.613, F.618, Y.651, G.869, Q.870, N.873, V.907, T.908, K.912 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:N.873 Hydrogen bonds: C:Q.870 BTI.4: 12 residues within 4Å: Chain B: K.1144 Chain D: Q.575, A.610, D.613, V.614, R.617, F.618, Y.651, N.873, T.908, S.911, K.912 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:V.614 Hydrogen bonds: D:T.908 BTI.5: 11 residues within 4Å: Chain A: A.610, D.613, V.614, R.617, R.644, Y.651, Q.870, T.908, S.911, K.912 Chain C: K.1144 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:K.1144, A:V.614 BTI.6: 11 residues within 4Å: Chain B: A.610, D.613, Y.651, G.869, Q.870, N.873, V.907, T.908, S.911, K.912 Chain D: K.1144 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.912 Hydrogen bonds: B:S.911, B:K.912

2 x ACO: ACETYL COENZYME *A(Non-covalent)

ACO.2: 25 residues within 4Å: Chain A: V.396, R.398, A.448, E.449, R.451, R.453, Q.494, N.495, R.496, A.497, Q.498, G.1055, K.1056, T.1057, R.1085 Chain B: F.53, R.54, T.57, R.77, Q.78, K.79, A.80, D.81, E.82, A.83 21 PLIP interactions: 5 interactions with chain B, 16 interactions with chain A Hydrophobic interactions: B:T.57, B:K.79 Hydrogen bonds: B:R.77, B:R.77, B:A.80, A:R.398, A:R.451, A:Q.494, A:N.495, A:R.496, A:Q.498, A:K.1056, A:T.1057 Salt bridges: A:R.398, A:R.453, A:R.453, A:R.453, A:R.496, A:K.1056, A:R.1085 pi-Cation interactions: A:K.1056 ACO.3: 21 residues within 4Å: Chain A: F.53, R.54, T.57, R.77, Q.78, K.79, A.80, D.81 Chain B: V.396, R.398, R.445, R.451, R.453, A.493, Q.494, N.495, R.496, K.1056, T.1057, N.1081, R.1085 19 PLIP interactions: 16 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.445, B:E.449, B:R.451, B:R.451, B:Q.494, B:N.495, B:R.496, B:K.1056, B:N.1081, A:Q.78, A:D.81, A:D.81 Salt bridges: B:R.398, B:R.451, B:R.453, B:R.453, B:R.453, B:R.496, B:R.1085

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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