SMTL ID : 8jxl.1

Human 3-methylcrotonyl-CoA carboxylase in MCCU state with MCoA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-mer

Ligands

6 x TW3: ~{S}-[2-[3-[[(2~{R})-4-[[[(2~{S},3~{S},4~{S},5~{S})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 3-methylbut-2-enethioate(Non-covalent)

TW3.1: 17 residues within 4Å: Chain A: R.78, K.141, G.142, A.144, G.174, G.175, A.176, Y.177, L.178, F.191, T.217, G.219 Chain C: G.446, Y.450, V.472, I.485, Q.489 14 PLIP interactions: 3 interactions with chain C, 11 interactions with chain A Hydrophobic interactions: C:Y.450, C:V.472, A:F.191, A:T.217 Hydrogen bonds: C:Q.489, A:K.141, A:K.141, A:G.174, A:A.176, A:A.176, A:L.178, A:G.219 Salt bridges: A:R.78, A:K.141 TW3.3: 17 residues within 4Å: Chain A: G.446, Y.450, V.472, I.485, Q.489 Chain C: R.78, K.141, G.142, A.144, G.174, G.175, A.176, Y.177, L.178, F.191, T.217, G.219 14 PLIP interactions: 11 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:F.191, C:T.217, A:Y.450, A:V.472 Hydrogen bonds: C:K.141, C:K.141, C:G.174, C:A.176, C:A.176, C:L.178, C:G.219, A:Q.489 Salt bridges: C:R.78, C:K.141 TW3.5: 17 residues within 4Å: Chain E: R.78, K.141, G.142, A.144, G.174, G.175, A.176, Y.177, L.178, F.191, T.217, G.219 Chain K: G.446, Y.450, V.472, I.485, Q.489 14 PLIP interactions: 11 interactions with chain E, 3 interactions with chain K Hydrophobic interactions: E:F.191, E:T.217, K:Y.450, K:V.472 Hydrogen bonds: E:K.141, E:K.141, E:G.174, E:A.176, E:A.176, E:L.178, E:G.219, K:Q.489 Salt bridges: E:R.78, E:K.141 TW3.7: 17 residues within 4Å: Chain G: R.78, K.141, G.142, A.144, G.174, G.175, A.176, Y.177, L.178, F.191, T.217, G.219 Chain I: G.446, Y.450, V.472, I.485, Q.489 12 PLIP interactions: 9 interactions with chain G, 3 interactions with chain I Hydrophobic interactions: G:F.191, G:T.217, I:Y.450, I:V.472 Hydrogen bonds: G:G.174, G:A.176, G:A.176, G:L.178, G:G.219, I:Q.489 Salt bridges: G:R.78, G:K.141 TW3.9: 17 residues within 4Å: Chain G: G.446, Y.450, V.472, I.485, Q.489 Chain I: R.78, K.141, G.142, A.144, G.174, G.175, A.176, Y.177, L.178, F.191, T.217, G.219 12 PLIP interactions: 9 interactions with chain I, 3 interactions with chain G Hydrophobic interactions: I:F.191, I:T.217, G:Y.450, G:V.472 Hydrogen bonds: I:G.174, I:A.176, I:A.176, I:L.178, I:G.219, G:Q.489 Salt bridges: I:R.78, I:K.141 TW3.11: 17 residues within 4Å: Chain E: G.446, Y.450, V.472, I.485, Q.489 Chain K: R.78, K.141, G.142, A.144, G.174, G.175, A.176, Y.177, L.178, F.191, T.217, G.219 14 PLIP interactions: 11 interactions with chain K, 3 interactions with chain E Hydrophobic interactions: K:F.191, K:T.217, E:Y.450, E:V.472 Hydrogen bonds: K:K.141, K:K.141, K:G.174, K:A.176, K:A.176, K:L.178, K:G.219, E:Q.489 Salt bridges: K:R.78, K:K.141

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

BTI.2: 1 residues within 4Å: Chain B: K.681 No protein-ligand interaction detected (PLIP) BTI.4: 1 residues within 4Å: Chain D: K.681 No protein-ligand interaction detected (PLIP) BTI.6: 1 residues within 4Å: Chain F: K.681 No protein-ligand interaction detected (PLIP) BTI.8: 1 residues within 4Å: Chain H: K.681 No protein-ligand interaction detected (PLIP) BTI.10: 1 residues within 4Å: Chain J: K.681 No protein-ligand interaction detected (PLIP) BTI.12: 1 residues within 4Å: Chain L: K.681 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, D.S. et al., Human 3-methylcrotonyl-CoA carboxylase in BCCP-BCS state with substrate. To Be Published

Release Date

2024-07-03

Peptides

Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial: ACEGIK
Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

C
A

E
D

G
G

I
I

K
K

B
F

D
C

F
E

H
H

J
J

L
L

Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial

Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial

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