SMTL ID : 8jxm.1

Human 3-methylcrotonyl-CoA carboxylase in BCCP-H2 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: 21 residues within 4Å: Chain A: R.78, K.141, G.142, A.144, G.174, G.175, A.176, Y.177, L.178, F.185, F.191, T.217, G.219 Chain E: G.446, A.447, Y.450, V.472, M.473, I.485, Q.489 Ligands: BTI.3 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain E Hydrophobic interactions: A:F.185, A:F.191, A:T.217, E:Y.450, E:V.472 Hydrogen bonds: A:K.141, A:K.141, A:G.174, A:A.176, A:A.176, A:L.178, A:G.219, E:Q.489 Salt bridges: A:R.78, A:K.141 TW3.2: 20 residues within 4Å: Chain C: R.78, K.141, G.142, A.144, G.174, G.175, A.176, Y.177, L.178, F.185, F.191, T.217, G.219 Chain H: G.446, A.447, Y.450, V.472, M.473, I.485, Q.489 15 PLIP interactions: 12 interactions with chain C, 3 interactions with chain H Hydrophobic interactions: C:F.185, C:F.191, C:T.217, H:Y.450, H: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, H:Q.489 Salt bridges: C:R.78, C:K.141 TW3.4: 17 residues within 4Å: Chain A: Y.450, V.472, I.485, Q.489 Chain E: R.78, K.141, G.142, A.144, G.174, G.175, A.176, Y.177, L.178, F.185, F.191, T.217, A.218 13 PLIP interactions: 10 interactions with chain E, 3 interactions with chain A Hydrophobic interactions: E:F.185, E:F.191, E:T.217, A:Y.450, A:V.472 Hydrogen bonds: E:K.141, E:G.174, E:A.176, E:A.176, E:L.178, A:Q.489 Salt bridges: E:R.78, E:K.141 TW3.8: 17 residues within 4Å: Chain C: Y.450, V.472, I.485, Q.489 Chain H: R.78, K.141, G.142, A.144, G.174, G.175, A.176, Y.177, L.178, F.185, F.191, T.217, A.218 13 PLIP interactions: 10 interactions with chain H, 3 interactions with chain C Hydrophobic interactions: H:F.185, H:F.191, H:T.217, C:Y.450, C:V.472 Hydrogen bonds: H:K.141, H:G.174, H:A.176, H:A.176, H:L.178, C:Q.489 Salt bridges: H:R.78, H:K.141 TW3.11: 16 residues within 4Å: Chain K: R.78, K.141, G.142, A.144, G.174, G.175, A.176, Y.177, L.178, F.191, T.217, A.218, G.219 Chain L: V.472, I.485, Q.489 12 PLIP interactions: 10 interactions with chain K, 2 interactions with chain L Hydrophobic interactions: K:F.191, K:T.217, L:V.472 Hydrogen bonds: K:K.141, K:G.174, K:A.176, K:A.176, K:L.178, K:G.219, L:Q.489 Salt bridges: K:R.78, K:K.141 TW3.12: 16 residues within 4Å: Chain K: V.472, I.485, Q.489 Chain L: R.78, K.141, G.142, A.144, G.174, G.175, A.176, Y.177, L.178, F.191, T.217, A.218, G.219 12 PLIP interactions: 10 interactions with chain L, 2 interactions with chain K Hydrophobic interactions: L:F.191, L:T.217, K:V.472 Hydrogen bonds: L:K.141, L:G.174, L:A.176, L:A.176, L:L.178, L:G.219, K:Q.489 Salt bridges: L:R.78, L:K.141

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

BTI.3: 14 residues within 4Å: Chain A: A.218, L.246 Chain D: K.681 Chain E: T.405, G.406, F.407, Y.445, G.446, A.447, G.448, V.472, M.473, G.474 Ligands: TW3.1 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:Y.445, E:M.473 Hydrogen bonds: E:F.407, E:F.407, E:A.447, E:G.448, E:G.474 BTI.5: 1 residues within 4Å: Chain F: K.681 No protein-ligand interaction detected (PLIP) BTI.6: 1 residues within 4Å: Chain G: K.681 No protein-ligand interaction detected (PLIP) BTI.7: 17 residues within 4Å: Chain B: M.680, K.681 Chain C: A.218, L.241, A.242, L.246, A.250 Chain H: T.405, G.406, F.407, V.409, Y.445, G.446, A.447, V.472, M.473, G.474 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:Y.445, H:M.473 Hydrogen bonds: H:G.474 BTI.9: 1 residues within 4Å: Chain I: K.681 No protein-ligand interaction detected (PLIP) BTI.10: 1 residues within 4Å: Chain J: K.681 No protein-ligand interaction detected (PLIP)

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

2024-07-03

Peptides

Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial: ACEHKL
Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial: BDFGIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

C
A

E
C

H
H

K
E

L
J

B
L

D
B

F
F

G
G

I
I

J
M

Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial

Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial

Related Entries With Identical Sequence