SMTL ID : 6ybq.1

Engineered glycolyl-CoA carboxylase (quintuple mutant) with bound CoA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-mer

Ligands

6 x COA: COENZYME A(Non-covalent)

COA.1: 14 residues within 4Å: Chain A: R.23, F.93, F.96, G.97, S.99, A.128, G.129, A.131, R.132, I.133, Q.134, Y.189 Chain B: I.438, R.441 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Salt bridges: B:R.441, A:R.23 Hydrogen bonds: A:A.131, A:I.133 Water bridges: A:F.96 COA.2: 13 residues within 4Å: Chain A: I.438, R.441 Chain B: R.23, F.93, F.96, G.97, S.99, G.129, A.131, R.132, I.133, Q.134, Y.189 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:R.441, B:R.23 Hydrogen bonds: B:A.131, B:I.133 COA.3: 15 residues within 4Å: Chain C: R.23, F.93, F.96, G.97, S.99, A.128, G.129, A.131, R.132, I.133, Q.134, Y.189, D.196 Chain D: I.438, R.441 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:A.131, C:I.133 Salt bridges: C:R.23, D:R.441 COA.4: 15 residues within 4Å: Chain C: I.438, R.441 Chain D: R.23, F.93, F.96, G.97, S.99, A.128, G.129, G.130, A.131, R.132, I.133, Q.134, Y.189 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.129, D:I.133 Water bridges: D:G.97 Salt bridges: D:R.23, C:R.441 COA.5: 14 residues within 4Å: Chain E: R.23, F.96, G.97, S.99, A.128, G.129, A.131, R.132, I.133, Q.134, Y.189, D.196 Chain F: I.438, R.441 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:Y.189 Hydrogen bonds: E:A.131, E:I.133 Salt bridges: E:R.23, F:R.441 COA.6: 13 residues within 4Å: Chain E: I.438, R.441 Chain F: R.23, F.96, G.97, S.99, G.129, A.131, R.132, I.133, Q.134, Y.189, D.196 6 PLIP interactions: 3 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:A.131, F:I.133, E:R.441, E:R.441 Salt bridges: F:R.23, E:R.441

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

BTI.7: 7 residues within 4Å: Chain A: V.332, P.362, G.363, F.364 Chain B: V.201 Chain G: M.632, K.633 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:F.364, A:F.364 Hydrophobic interactions: B:V.201 BTI.8: 6 residues within 4Å: Chain C: V.332, G.363, F.364 Chain D: V.201 Chain H: M.632, K.633 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:F.364, C:F.364 Hydrophobic interactions: D:V.201 BTI.9: 6 residues within 4Å: Chain E: V.332, P.362, F.364 Chain F: V.197 Chain I: M.632, K.633 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:F.364, E:F.364 BTI.10: 8 residues within 4Å: Chain A: T.193, V.201 Chain B: V.332, P.362, G.363, F.364 Chain J: M.632, K.633 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.201 Hydrogen bonds: B:F.364, B:F.364 BTI.11: 7 residues within 4Å: Chain E: T.193 Chain F: V.332, P.362, G.363, F.364 Chain K: M.632, K.633 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:F.364 Water bridges: F:F.364, F:F.364 BTI.12: 6 residues within 4Å: Chain C: V.201 Chain D: V.332, G.363, F.364 Chain L: M.632, K.633 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:V.201 Hydrogen bonds: D:F.364 Water bridges: D:F.364, D:F.364

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Scheffen, M. et al., A new-to-nature carboxylation module to improve natural and synthetic CO2 fixation. Nat Catal (2021)

Release Date

2020-10-28

Peptides

Propionyl-CoA carboxylase beta chain: ABCDEF
Propionyl-CoA carboxylase alpha subunit: GHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

Propionyl-CoA carboxylase beta chain

Propionyl-CoA carboxylase alpha subunit

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