SMTL ID : 7wtb.1

Cryo-EM structure of human pyruvate carboxylase with acetyl-CoA

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: 9 residues within 4Å: Chain A: K.1144 Chain C: D.613, Y.651, G.869, Q.870, V.907, T.908, S.911, K.912 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.870, C:V.907, C:S.911 BTI.5: 12 residues within 4Å: Chain B: K.1144 Chain D: Q.575, A.610, D.613, R.617, F.618, Y.651, Q.870, N.873, T.908, S.911, K.912 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:N.873 Hydrogen bonds: D:R.617, D:T.908, D:S.911 BTI.7: 11 residues within 4Å: Chain A: D.613, R.617, F.618, Y.651, G.869, Q.870, N.873, T.908, S.911, K.912 Chain C: K.1144 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.870, A:S.911, A:S.911 BTI.8: 9 residues within 4Å: Chain B: D.613, R.644, Y.651, Q.870, N.873, T.908, S.911, K.912 Chain D: K.1144 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.907, B:T.908, B:S.911, B:K.912, B:K.912

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.2: 11 residues within 4Å: Chain A: G.199, G.201, M.204, K.237, F.238, I.239, P.242, H.271, K.273, E.324, N.326 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.239, A:I.239, A:H.271, A:E.324, A:N.326 Salt bridges: A:K.273 ANP.6: 19 residues within 4Å: Chain B: I.192, K.194, G.198, G.199, G.200, G.201, M.204, E.236, K.237, F.238, I.239, P.242, H.244, Q.268, H.271, E.311, L.313, I.323, E.324 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.200, B:G.200, B:K.237, B:I.239, B:H.244, B:Q.268 Salt bridges: B:K.194

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

ACO.3: 21 residues within 4Å: Chain A: R.398, R.445, E.449, R.451, R.453, Q.494, N.495, R.496, A.497, K.1056, T.1057, L.1058, L.1080 Chain B: F.53, R.54, T.57, R.77, Q.78, K.79, A.80, D.81 17 PLIP interactions: 11 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:R.451, A:Q.494, A:N.495, A:K.1056, A:R.1085, B:R.77, B:R.77, B:A.80, B:D.81 Salt bridges: A:R.398, A:R.451, A:R.453, A:R.453, A:K.1056 pi-Cation interactions: A:K.1056 Hydrophobic interactions: B:F.53, B:K.79 ACO.4: 21 residues within 4Å: Chain A: F.53, R.54, T.57, R.77, Q.78, K.79, A.80, D.81 Chain B: R.398, R.445, A.448, E.449, R.451, R.453, A.493, Q.494, N.495, R.496, K.1056, T.1057, R.1085 16 PLIP interactions: 14 interactions with chain B, 2 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, A:A.80 Salt bridges: B:R.398, B:R.451, B:R.453, B:R.453, B:R.496, B:R.1085 Hydrophobic interactions: A:F.53

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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