SMTL ID : 8pn7.1

Engineered glycolyl-CoA carboxylase (G20R variant) 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: 16 residues within 4Å: Chain A: R.23, F.96, G.97, S.99, A.128, G.129, A.131, R.132, I.133, Q.134, P.166, A.168, Y.189, D.196 Chain B: I.438, R.441 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.166, A:Y.189 Hydrogen bonds: A:S.99, A:A.131, A:I.133 Water bridges: A:G.97 Salt bridges: A:R.23, B:R.441 COA.2: 16 residues within 4Å: Chain A: I.438, R.441 Chain B: R.23, F.96, G.97, S.99, A.128, G.129, A.131, R.132, I.133, Q.134, P.166, A.168, Y.189, D.196 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.166, B:Y.189 Hydrogen bonds: B:S.99, B:A.131, B:I.133, B:Y.189 Water bridges: B:R.23, B:R.23, B:G.97 Salt bridges: B:R.23, A:R.441 COA.3: 16 residues within 4Å: Chain C: R.23, F.96, G.97, S.99, A.128, G.129, A.131, R.132, I.133, Q.134, P.166, A.168, Y.189, D.196 Chain D: I.438, R.441 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:P.166, C:Y.189 Hydrogen bonds: C:S.99, C:A.131, C:I.133 Water bridges: C:G.97 Salt bridges: C:R.23, D:R.441 COA.4: 16 residues within 4Å: Chain C: I.438, R.441 Chain D: R.23, F.96, G.97, S.99, A.128, G.129, A.131, R.132, I.133, Q.134, P.166, A.168, Y.189, D.196 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:P.166, D:Y.189 Hydrogen bonds: D:S.99, D:A.131, D:I.133, D:Y.189 Water bridges: D:G.97 Salt bridges: D:R.23, C:R.441 COA.5: 16 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, P.166, A.168, Y.189, D.196 Chain F: I.438, R.441 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:P.166, E:Y.189 Hydrogen bonds: E:S.99, E:A.131, E:I.133 Water bridges: E:G.97 Salt bridges: E:R.23, F:R.441 COA.6: 16 residues within 4Å: Chain E: I.438, R.441 Chain F: R.23, F.96, G.97, S.99, A.128, G.129, A.131, R.132, I.133, Q.134, P.166, A.168, Y.189, D.196 8 PLIP interactions: 7 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:P.166, F:Y.189 Hydrogen bonds: F:S.99, F:A.131, F:I.133, F:Y.189 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: 9 residues within 4Å: Chain A: V.332, P.362, G.363, F.364 Chain B: T.193, V.197, V.201 Chain G: M.632, K.633 6 PLIP interactions: 1 interactions with chain G, 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: G:K.633, B:V.197, B:V.201 Hydrogen bonds: A:F.364, B:T.193 Water bridges: A:F.364 BTI.8: 9 residues within 4Å: Chain C: V.332, P.362, G.363, F.364 Chain D: T.193, V.197, V.201 Chain H: M.632, K.633 6 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D, 1 interactions with chain H Hydrogen bonds: C:F.364, C:F.364, D:T.193 Hydrophobic interactions: D:V.197, D:V.201, H:K.633 BTI.9: 9 residues within 4Å: Chain E: V.332, P.362, G.363, F.364 Chain F: T.193, V.197, V.201 Chain I: M.632, K.633 6 PLIP interactions: 2 interactions with chain E, 3 interactions with chain F, 1 interactions with chain I Hydrogen bonds: E:F.364, E:F.364, F:T.193 Hydrophobic interactions: F:V.197, F:V.201, I:K.633 BTI.10: 10 residues within 4Å: Chain A: T.193, V.197, T.200, V.201 Chain B: V.332, P.362, G.363, F.364 Chain J: M.632, K.633 6 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B, 1 interactions with chain J Hydrophobic interactions: A:V.197, A:T.200, A:V.201, J:K.633 Hydrogen bonds: B:F.364, B:F.364 BTI.11: 9 residues within 4Å: Chain E: T.193, V.197, V.201 Chain F: V.332, P.362, G.363, F.364 Chain K: M.632, K.633 4 PLIP interactions: 1 interactions with chain F, 1 interactions with chain K, 2 interactions with chain E Hydrogen bonds: F:F.364 Hydrophobic interactions: K:K.633, E:V.197, E:V.201 BTI.12: 9 residues within 4Å: Chain C: T.193, V.197, V.201 Chain D: V.332, P.362, G.363, F.364 Chain L: M.632, K.633 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain L, 2 interactions with chain D Hydrophobic interactions: C:V.197, C:V.201, L:K.633 Hydrogen bonds: D:F.364, D:F.364

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marchal, D.G. et al., Machine Learning-Supported Enzyme Engineering toward Improved CO 2 -Fixation of Glycolyl-CoA Carboxylase. Acs Synth Biol (2023)

Release Date

2023-11-29

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

Related Entries With Identical Sequence