SMTL ID : 8j4z.1

Human 3-methylcrotonyl-CoA carboxylase in BCCP-CTS state with substrate

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: 14 residues within 4Å: Chain A: G.406, F.407, V.409, Y.445, G.446, A.447, G.448 Chain B: M.680, K.681 Chain I: A.218, L.241, L.246, A.250 Ligands: TW3.9 7 PLIP interactions: 1 interactions with chain B, 2 interactions with chain I, 4 interactions with chain A Hydrophobic interactions: B:K.681, I:L.246, I:A.250 Hydrogen bonds: A:F.407, A:F.407, A:A.447, A:G.448 BTI.3: 14 residues within 4Å: Chain C: G.406, F.407, V.409, Y.445, G.446, A.447, G.448 Chain D: M.680, K.681 Chain K: A.218, L.241, L.246, A.250 Ligands: TW3.11 6 PLIP interactions: 2 interactions with chain K, 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: K:L.246, K:A.250, D:K.681 Hydrogen bonds: C:F.407, C:A.447, C:G.448 BTI.5: 14 residues within 4Å: Chain E: G.406, F.407, V.409, Y.445, G.446, A.447, G.448 Chain F: M.680, K.681 Chain G: A.218, L.241, L.246, A.250 Ligands: TW3.7 7 PLIP interactions: 1 interactions with chain F, 4 interactions with chain E, 2 interactions with chain G Hydrophobic interactions: F:K.681, G:L.246, G:A.250 Hydrogen bonds: E:F.407, E:F.407, E:A.447, E:G.448 BTI.8: 13 residues within 4Å: Chain E: A.218, L.241, L.246, A.250 Chain G: G.406, F.407, Y.445, G.446, A.447, G.448 Chain H: M.680, K.681 Ligands: TW3.6 7 PLIP interactions: 4 interactions with chain G, 2 interactions with chain E, 1 interactions with chain H Hydrogen bonds: G:F.407, G:F.407, G:A.447, G:G.448 Hydrophobic interactions: E:L.246, E:A.250, H:K.681 BTI.10: 14 residues within 4Å: Chain A: A.218, L.241, L.246, A.250 Chain I: G.406, F.407, V.409, Y.445, G.446, A.447, G.448 Chain J: M.680, K.681 Ligands: TW3.2 7 PLIP interactions: 4 interactions with chain I, 2 interactions with chain A, 1 interactions with chain J Hydrogen bonds: I:F.407, I:F.407, I:A.447, I:G.448 Hydrophobic interactions: A:L.246, A:A.250, J:K.681 BTI.12: 14 residues within 4Å: Chain C: A.218, L.241, L.246, A.250 Chain K: G.406, F.407, V.409, Y.445, G.446, A.447, G.448 Chain L: M.680, K.681 Ligands: TW3.4 7 PLIP interactions: 4 interactions with chain K, 2 interactions with chain C, 1 interactions with chain L Hydrogen bonds: K:F.407, K:F.407, K:A.447, K:G.448 Hydrophobic interactions: C:L.246, C:A.250, L:K.681

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

TW3.2: 20 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, S.215, T.217, A.218, G.219 Chain I: M.473, V.481, I.485, Q.489, R.492 Ligands: BTI.10 14 PLIP interactions: 5 interactions with chain I, 9 interactions with chain A Hydrogen bonds: I:Q.489, I:Q.489, I:Q.489, A:K.141, A:G.174, A:A.176, A:L.178, A:T.217 Salt bridges: I:R.492, I:R.492, A:R.78, A:K.141 Hydrophobic interactions: A:F.191, A:T.217 TW3.4: 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.191, S.215, T.217, A.218, G.219 Chain K: M.473, V.481, I.485, Q.489, R.492 Ligands: BTI.12 14 PLIP interactions: 9 interactions with chain C, 5 interactions with chain K Hydrophobic interactions: C:F.191, C:T.217 Hydrogen bonds: C:K.141, C:G.174, C:A.176, C:L.178, C:T.217, K:Q.489, K:Q.489, K:Q.489 Salt bridges: C:R.78, C:K.141, K:R.492, K:R.492 TW3.6: 20 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, S.215, T.217, A.218, G.219 Chain G: M.473, V.481, I.485, Q.489, R.492 Ligands: BTI.8 14 PLIP interactions: 9 interactions with chain E, 5 interactions with chain G Hydrophobic interactions: E:F.191, E:T.217 Hydrogen bonds: E:K.141, E:G.174, E:A.176, E:L.178, E:T.217, G:Q.489, G:Q.489, G:Q.489 Salt bridges: E:R.78, E:K.141, G:R.492, G:R.492 TW3.7: 20 residues within 4Å: Chain E: M.473, V.481, 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, S.215, T.217, A.218, G.219 Ligands: BTI.5 13 PLIP interactions: 8 interactions with chain G, 5 interactions with chain E Hydrophobic interactions: G:F.191, G:T.217 Hydrogen bonds: G:K.141, G:G.174, G:A.176, G:L.178, E:Q.489, E:Q.489, E:Q.489 Salt bridges: G:R.78, G:K.141, E:R.492, E:R.492 TW3.9: 20 residues within 4Å: Chain A: M.473, V.481, I.485, Q.489, R.492 Chain I: R.78, K.141, G.142, A.144, G.174, G.175, A.176, Y.177, L.178, F.191, S.215, T.217, A.218, G.219 Ligands: BTI.1 13 PLIP interactions: 8 interactions with chain I, 5 interactions with chain A Hydrophobic interactions: I:F.191, I:T.217 Hydrogen bonds: I:K.141, I:G.174, I:A.176, I:L.178, A:Q.489, A:Q.489, A:Q.489 Salt bridges: I:R.78, I:K.141, A:R.492, A:R.492 TW3.11: 20 residues within 4Å: Chain C: M.473, V.481, I.485, Q.489, R.492 Chain K: R.78, K.141, G.142, A.144, G.174, G.175, A.176, Y.177, L.178, F.191, S.215, T.217, A.218, G.219 Ligands: BTI.3 13 PLIP interactions: 8 interactions with chain K, 5 interactions with chain C Hydrophobic interactions: K:F.191, K:T.217 Hydrogen bonds: K:K.141, K:G.174, K:A.176, K:L.178, C:Q.489, C:Q.489, C:Q.489 Salt bridges: K:R.78, K:K.141, C:R.492, C:R.492

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2024-04-24

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
J

C
A

E
C

G
F

I
H

K
K

B
E

D
B

F
D

H
G

J
I

L
L

Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial

Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial

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