8I01

Crystal structure of Escherichia coli glyoxylate carboligase

PDB DOI: https://doi.org/10.2210/pdb8I01/pdb

Classification: LIGASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-01-10 Released: 2023-11-22
Deposition Author(s): Kim, J.H., Kim, J.S.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.231
R-Value Work: 0.191
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Engineering of two thiamine diphosphate-dependent enzymes for the regioselective condensation of C1-formaldehyde into C4-erythrulose

Kim, J.H., Cheon, H., Jo, H.J., Kim, J.W., Kim, G.Y., Seo, H.R., Seo, P.W., Kim, J.S., Park, J.B.

(2023) Int J Biol Macromol 253: 127674

DOI: https://doi.org/10.1016/j.ijbiomac.2023.127674

Macromolecule Content

Total Structure Weight: 398.74 kDa
Atom Count: 30,468
Modelled Residue Count: 3,562
Deposited Residue Count: 3,564
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxylate carboligase	A, B, C, D, E A, B, C, D, E, F	594	Escherichia coli K-12	Mutation(s): 1 Gene Names: gcl, b0507, JW0495 EC: 4.1.1.47
UniProt
Find proteins for P0AEP7 (Escherichia coli (strain K12)) Explore P0AEP7 Go to UniProtKB: P0AEP7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AEP7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain FA [auth E] SDF format, chain G [auth A] SDF format, chain KA [auth F] SDF format, chain M [auth B] SDF format, chain S [auth C] SDF format, chain Y [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain M [auth B] MOL2 format, chain S [auth C] MOL2 format, chain Y [auth D]	FA [auth E] G [auth A] KA [auth F] M [auth B] S [auth C] FA [auth E], G [auth A], KA [auth F], M [auth B], S [auth C], Y [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain FA [auth E] Focus chain G [auth A] Focus chain KA [auth F] Focus chain M [auth B] Focus chain S [auth C] Focus chain Y [auth D] Interactions & Density Focus chain FA [auth E] Focus chain G [auth A] Focus chain KA [auth F] Focus chain M [auth B] Focus chain S [auth C] Focus chain Y [auth D]
TPP (Subject of Investigation/LOI) Query on TPP Download Ideal Coordinates CCD File SDF format, chain GA [auth E] SDF format, chain H [auth A] SDF format, chain LA [auth F] SDF format, chain N [auth B] SDF format, chain T [auth C] SDF format, chain Z [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain H [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Z [auth D]	GA [auth E] H [auth A] LA [auth F] N [auth B] T [auth C] GA [auth E], H [auth A], LA [auth F], N [auth B], T [auth C], Z [auth D]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain GA [auth E] Focus chain H [auth A] Focus chain LA [auth F] Focus chain N [auth B] Focus chain T [auth C] Focus chain Z [auth D] Interactions & Density Focus chain GA [auth E] Focus chain H [auth A] Focus chain LA [auth F] Focus chain N [auth B] Focus chain T [auth C] Focus chain Z [auth D]
UQ0 (Subject of Investigation/LOI) Query on UQ0 Download Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain NA [auth F] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain JA [auth E] SDF format, chain X [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain JA [auth E] MOL2 format, chain X [auth C]	CA [auth D] DA [auth D] EA [auth D] JA [auth E] K [auth A] CA [auth D], DA [auth D], EA [auth D], JA [auth E], K [auth A], L [auth A], NA [auth F], Q [auth B], R [auth B], V [auth C], W [auth C], X [auth C]	2,3-DIMETHOXY-5-METHYL-1,4-BENZOQUINONE C₉ H₁₀ O₄ UIXPTCZPFCVOQF-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain JA [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain NA [auth F] Focus chain Q [auth B] Focus chain R [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain JA [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain NA [auth F] Focus chain Q [auth B] Focus chain R [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain HA [auth E] SDF format, chain I [auth A] SDF format, chain IA [auth E] SDF format, chain J [auth A] SDF format, chain MA [auth F] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain U [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C]	AA [auth D] BA [auth D] HA [auth E] I [auth A] IA [auth E] AA [auth D], BA [auth D], HA [auth E], I [auth A], IA [auth E], J [auth A], MA [auth F], O [auth B], P [auth B], U [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain MA [auth F] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain MA [auth F] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C]