8RYB | pdb_00008ryb

CryoEM structure of M. smegmatis GMP reductase in complex with GMP at pH 7.8, extended conformation.

PDB DOI: https://doi.org/10.2210/pdb8RYB/pdb
EM Map EMD-19593: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Mycolicibacterium smegmatis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-02-08 Released: 2025-08-20
Deposition Author(s): Dolezal, M., Tomas, K., Filimonenko, A., Pichova, I.
Funding Organization(s): European Union (EU)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.84 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Structural basis for allosteric regulation of mycobacterial guanosine 5'-monophosphate reductase with ATP and GTP.

Dolezal, M., Knejzlik, Z., Kouba, T., Filimonenko, A., Svachova, H., Klima, M., Pichova, I.

To be published.

Macromolecule Content

Total Structure Weight: 420.07 kDa
Atom Count: 27,736
Modeled Residue Count: 3,752
Deposited Residue Count: 3,968
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GMP reductase	A, B, C, D, E A, B, C, D, E, F, G, H	496	Mycolicibacterium smegmatis	Mutation(s): 0 Gene Names: guaB1, MSMEG_3634, MSMEI_3548 EC: 1.7.1.7
UniProt
Find proteins for A0QYE8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QYE8 Go to UniProtKB: A0QYE8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0QYE8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5GP (Subject of Investigation/LOI) Query on 5GP Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain Q [auth E] SDF format, chain R [auth E] SDF format, chain S [auth F] SDF format, chain T [auth F] SDF format, chain U [auth G] SDF format, chain V [auth G] SDF format, chain W [auth H] SDF format, chain X [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth E] MOL2 format, chain S [auth F] MOL2 format, chain T [auth F] MOL2 format, chain U [auth G] MOL2 format, chain V [auth G] MOL2 format, chain W [auth H] MOL2 format, chain X [auth H] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth E] mmCIF format, chain S [auth F] mmCIF format, chain T [auth F] mmCIF format, chain U [auth G] mmCIF format, chain V [auth G] mmCIF format, chain W [auth H] mmCIF format, chain X [auth H]	I [auth A] J [auth A] K [auth B] L [auth B] M [auth C] I [auth A], J [auth A], K [auth B], L [auth B], M [auth C], N [auth C], O [auth D], P [auth D], Q [auth E], R [auth E], S [auth F], T [auth F], U [auth G], V [auth G], W [auth H], X [auth H]	GUANOSINE-5'-MONOPHOSPHATE C₁₀ H₁₄ N₅ O₈ P RQFCJASXJCIDSX-UUOKFMHZSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth H]