SMTL ID : 8jxn.1

Human 3-methylcrotonyl-CoA carboxylase in BCCP-H1 state with MCoA

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: 15 residues within 4Å: Chain A: T.405, G.406, F.407, Y.445, G.446, A.447, V.472, M.473, G.474, Q.477 Chain E: M.680, K.681 Chain K: A.218, L.246 Ligands: TW3.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.407, A:F.407, A:A.447, A:G.474 BTI.3: 1 residues within 4Å: Chain B: K.681 No protein-ligand interaction detected (PLIP) BTI.4: 1 residues within 4Å: Chain C: K.681 No protein-ligand interaction detected (PLIP) BTI.5: 16 residues within 4Å: Chain D: T.405, G.406, F.407, V.409, Y.445, G.446, A.447, V.472, M.473, G.474, Q.477 Chain F: M.680, K.681 Chain G: A.218, A.242, L.246 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain G Hydrophobic interactions: D:Y.445, D:M.473, G:L.246 Hydrogen bonds: D:F.407, D:G.474 BTI.8: 14 residues within 4Å: Chain D: A.218, L.246 Chain G: T.405, G.406, F.407, Y.445, G.446, A.447, G.448, G.474, Q.477 Chain I: M.680, K.681 Ligands: TW3.6 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:F.407, G:F.407, G:A.447, G:G.448, G:G.474 BTI.9: 16 residues within 4Å: Chain H: M.680, K.681 Chain J: T.405, G.406, F.407, V.409, Y.445, G.446, A.447, V.472, M.473, G.474, Q.477 Chain L: A.218, L.241, L.246 4 PLIP interactions: 4 interactions with chain J Hydrophobic interactions: J:M.473 Hydrogen bonds: J:F.407, J:F.407, J:G.474

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)

TW3.2: 19 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, A.218 Chain K: G.446, A.447, Y.450, V.472, I.485, Q.489 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain K Hydrophobic interactions: A:F.185, A:F.191, A:T.217, K:Y.450, K:V.472 Hydrogen bonds: A:K.141, A:G.174, A:A.176, A:A.176, A:L.178, A:T.217, K:Q.489 Salt bridges: A:R.78, A:K.141 TW3.6: 19 residues within 4Å: Chain D: 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 G: G.446, Y.450, V.472, I.485, Q.489, R.492 Ligands: BTI.8 14 PLIP interactions: 9 interactions with chain D, 5 interactions with chain G Hydrophobic interactions: D:F.191, D:T.217, G:Y.450, G:V.472 Hydrogen bonds: D:G.174, D:A.176, D:A.176, D:L.178, D:G.219, G:Q.489 Salt bridges: D:R.78, D:K.141, G:R.492, G:R.492 TW3.7: 18 residues within 4Å: Chain D: G.446, Y.450, V.472, I.485, Q.489, R.492 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 14 PLIP interactions: 9 interactions with chain G, 5 interactions with chain D Hydrophobic interactions: G:F.191, G:T.217, D:Y.450, D:V.472 Hydrogen bonds: G:G.174, G:A.176, G:A.176, G:L.178, G:G.219, D:Q.489 Salt bridges: G:R.78, G:K.141, D:R.492, D:R.492 TW3.10: 18 residues within 4Å: Chain J: 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 Chain L: G.446, Y.450, V.472, I.485, Q.489 14 PLIP interactions: 11 interactions with chain J, 3 interactions with chain L Hydrophobic interactions: J:F.185, J:F.191, J:T.217, L:Y.450, L:V.472 Hydrogen bonds: J:K.141, J:G.174, J:A.176, J:A.176, J:L.178, J:T.217, L:Q.489 Salt bridges: J:R.78, J:K.141 TW3.11: 20 residues within 4Å: Chain A: 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.185, F.191, T.217, A.218, G.219 Ligands: BTI.1 14 PLIP interactions: 11 interactions with chain K, 3 interactions with chain A Hydrophobic interactions: K:F.185, K:F.191, K:T.217, A:Y.450, A:V.472 Hydrogen bonds: K:K.141, K:G.174, K:A.176, K:A.176, K:L.178, K:G.219, A:Q.489 Salt bridges: K:R.78, K:K.141 TW3.12: 19 residues within 4Å: Chain J: G.446, A.447, Y.450, V.472, M.473, 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, G.219 12 PLIP interactions: 3 interactions with chain J, 9 interactions with chain L Hydrophobic interactions: J:Y.450, J:V.472, L:F.191, L:T.217 Hydrogen bonds: J:Q.489, L:G.174, L:A.176, L:A.176, L:L.178, L:G.219 Salt bridges: L:R.78, L:K.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, D.S. et al., Human 3-methylcrotonyl-CoA carboxylase in BCCP-H1 state with substrate. To Be Published

Release Date

2024-07-03

Peptides

Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial: ADGJKL
Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial: BCEFHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

D
G

G
I

J
B

K
K

L
A

B
E

C
F

E
H

F
C

H
J

I
L

Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial

Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial

Related Entries With Identical Sequence