8EBC | pdb_00008ebc

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Listeria monocytogenes in the complex with IMP

PDB DOI: https://doi.org/10.2210/pdb8EBC/pdb

Classification: OXIDOREDUCTASE
Organism(s): Listeria monocytogenes EGD-e
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-08-31 Released: 2022-09-07
Deposition Author(s): Kim, Y., Maltseva, N., Makowska-Grzyska, M., Osipiuk, J., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID), Center for Structural Biology of Infectious Diseases (CSBID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.239 (Depositor), 0.239 (DCC)
R-Value Work:
0.194 (Depositor), 0.194 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Listeria monocytogenes in the complex with IMP

Kim, Y., Maltseva, N., Makowska-Grzyska, M., Osipiuk, J., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 260.75 kDa
Atom Count: 16,120
Modeled Residue Count: 2,060
Deposited Residue Count: 2,370
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lmo0132 protein	A B C D E [auth F] A, B, C, D, E [auth F], F [auth E]	395	Listeria monocytogenes EGD-e	Mutation(s): 0 Gene Names: lmo0132
UniProt
Find proteins for Q8YAJ3 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8YAJ3 Go to UniProtKB: Q8YAJ3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8YAJ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IMP (Subject of Investigation/LOI) Query on IMP Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain L [auth D] SDF format, chain M [auth F] SDF format, chain O [auth E] SDF format, chain K [auth C] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth D] MOL2 format, chain M [auth F] MOL2 format, chain O [auth E] MOL2 format, chain K [auth C] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth D] mmCIF format, chain M [auth F] mmCIF format, chain O [auth E] mmCIF format, chain K [auth C]	G [auth A] J [auth B] K [auth C] L [auth D] M [auth F] G [auth A], J [auth B], K [auth C], L [auth D], M [auth F], O [auth E]	INOSINIC ACID C₁₀ H₁₃ N₄ O₈ P GRSZFWQUAKGDAV-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth F] Focus chain O [auth E] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth F] Focus chain O [auth E]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain N [auth F] MOL2 format, chain I [auth A] MOL2 format, chain N [auth F] mmCIF format, chain I [auth A] mmCIF format, chain N [auth F]	I [auth A], N [auth F]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain N [auth F] Interactions & Density Focus chain I [auth A] Focus chain N [auth F]