SMTL ID : 8k2v.1

3-Methylcrotonyl-CoA Carboxylase in MCCD state with Acetyl CoA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-mer

Ligands

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

BTI.1: 7 residues within 4Å: Chain A: M.680, K.681 Chain K: A.250 Chain L: G.406, F.407, E.476, Q.477 6 PLIP interactions: 5 interactions with chain L, 1 interactions with chain A Hydrophobic interactions: L:Q.477, A:K.681 Hydrogen bonds: L:F.407, L:F.407, L:Q.477, L:Q.477 BTI.2: 8 residues within 4Å: Chain B: M.680, K.681 Chain G: A.249, A.250 Chain H: G.406, F.407, E.476, Q.477 5 PLIP interactions: 4 interactions with chain H, 1 interactions with chain B Hydrophobic interactions: H:Q.477, B:K.681 Hydrogen bonds: H:F.407, H:Q.477, H:Q.477 BTI.3: 7 residues within 4Å: Chain C: M.680, K.681 Chain K: G.406, F.407, Q.477 Chain L: A.250, T.251 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain C Hydrogen bonds: K:F.407, K:F.407, K:Q.477 Hydrophobic interactions: C:K.681 BTI.4: 9 residues within 4Å: Chain D: M.680, K.681 Chain I: A.249, A.250, T.251 Chain J: G.406, F.407, V.409, Q.477 5 PLIP interactions: 4 interactions with chain J, 1 interactions with chain D Hydrophobic interactions: J:Q.477, D:K.681 Hydrogen bonds: J:F.407, J:Q.477, J:Q.477 BTI.5: 8 residues within 4Å: Chain E: M.680, K.681 Chain I: G.406, F.407, Q.477 Chain J: A.249, A.250, T.251 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain I Hydrophobic interactions: E:K.681 Hydrogen bonds: I:F.407, I:F.407, I:Q.477 BTI.6: 9 residues within 4Å: Chain F: M.680, K.681 Chain G: G.406, F.407, V.409, Q.477 Chain H: A.249, A.250, T.251 4 PLIP interactions: 1 interactions with chain F, 2 interactions with chain G, 1 interactions with chain H Hydrophobic interactions: F:K.681, G:Q.477, H:A.250 Hydrogen bonds: G:F.407

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

ACO.7: 13 residues within 4Å: Chain G: A.138, K.141, G.142, A.144, G.174, G.175, A.176, Y.177, L.178, T.217, A.218 Chain H: I.485, Q.489 8 PLIP interactions: 1 interactions with chain H, 7 interactions with chain G Hydrogen bonds: H:Q.489, G:R.78, G:K.141, G:G.142, G:A.176, G:L.178 Hydrophobic interactions: G:T.217 Salt bridges: G:K.141 ACO.8: 14 residues within 4Å: Chain G: I.485, Q.489 Chain H: R.78, A.138, K.141, G.142, A.144, G.174, G.175, A.176, Y.177, L.178, T.217, A.218 10 PLIP interactions: 9 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:T.217, H:A.218 Hydrogen bonds: H:K.141, H:G.142, H:A.176, H:L.178, H:T.217, G:Q.489 Salt bridges: H:R.78, H:K.141 ACO.9: 12 residues within 4Å: Chain I: R.78, A.138, K.141, G.142, A.144, G.174, G.175, A.176, Y.177, L.178, T.217 Chain J: Q.489 8 PLIP interactions: 1 interactions with chain J, 7 interactions with chain I Hydrogen bonds: J:Q.489, I:K.141, I:G.142, I:G.175, I:A.176, I:L.178 Salt bridges: I:R.78, I:K.141 ACO.10: 16 residues within 4Å: Chain I: I.485, Q.489 Chain J: R.78, K.141, G.142, A.144, D.172, S.173, G.174, G.175, A.176, Y.177, L.178, S.215, T.217, A.218 10 PLIP interactions: 9 interactions with chain J, 1 interactions with chain I Hydrophobic interactions: J:A.218 Hydrogen bonds: J:K.141, J:A.176, J:L.178, J:S.215, J:T.217, J:T.217, I:Q.489 Salt bridges: J:R.78, J:K.141 ACO.11: 13 residues within 4Å: Chain K: R.78, A.138, K.141, G.142, A.144, G.174, G.175, A.176, Y.177, L.178, T.217 Chain L: I.485, Q.489 9 PLIP interactions: 8 interactions with chain K, 1 interactions with chain L Hydrogen bonds: K:K.141, K:G.142, K:G.175, K:A.176, K:L.178, K:T.217, L:Q.489 Salt bridges: K:R.78, K:K.141 ACO.12: 13 residues within 4Å: Chain K: I.485, Q.489 Chain L: R.78, A.138, K.141, G.142, A.144, G.174, G.175, A.176, L.178, T.217, A.218 9 PLIP interactions: 8 interactions with chain L, 1 interactions with chain K Hydrophobic interactions: L:A.218 Hydrogen bonds: L:K.141, L:G.142, L:G.175, L:L.178, L:T.217, K:Q.489 Salt bridges: L:R.78, L:K.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Su, J. et al., Structural insight into synergistic activation of human 3-methylcrotonyl-CoA carboxylase. Nat.Struct.Mol.Biol. (2024)

Release Date

2024-07-10

Peptides

Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial: ABCDEF
Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial: GHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
I

I
J

J
K

K
L

L
H

Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial

Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial

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