9HG0 | pdb_00009hg0

Crystal structure of M. smegmatis GMP reductase with XMP* intermidiate in complex with NADP+ and IMP.

PDB DOI: https://doi.org/10.2210/pdb9HG0/pdb

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

Deposited: 2024-11-18 Released: 2025-08-27
Deposition Author(s): Dolezal, M., Pichova, I.
Funding Organization(s): European Union (EU)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.248 (Depositor), 0.248 (DCC)
R-Value Work:
0.218 (Depositor), 0.218 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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: 425.78 kDa
Atom Count: 28,877
Modeled Residue Count: 3,784
Deposited Residue Count: 3,968
Unique protein chains: 1

Macromolecules

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(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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP (Subject of Investigation/LOI) Query on NAP Download Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain S [auth D] SDF format, chain V [auth E] SDF format, chain Y [auth F] SDF format, chain DA [auth G] MOL2 format, chain BA [auth G] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] MOL2 format, chain V [auth E] MOL2 format, chain Y [auth F] MOL2 format, chain DA [auth G] mmCIF format, chain BA [auth G] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D] mmCIF format, chain V [auth E] mmCIF format, chain Y [auth F] mmCIF format, chain DA [auth G]	BA [auth G] DA [auth G] J [auth A] M [auth B] P [auth C] BA [auth G], DA [auth G], J [auth A], M [auth B], P [auth C], S [auth D], V [auth E], Y [auth F]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain BA [auth G] Focus chain DA [auth G] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Y [auth F] Interactions & Density Focus chain BA [auth G] Focus chain DA [auth G] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Y [auth F]
IMP (Subject of Investigation/LOI) Query on IMP Download Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain EA [auth H] SDF format, chain FA [auth H] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain L [auth B] SDF format, chain N [auth B] SDF format, chain O [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth D] SDF format, chain W [auth E] SDF format, chain Z [auth F] SDF format, chain X [auth F] SDF format, chain U [auth E] SDF format, chain T [auth D] SDF format, chain AA [auth G] MOL2 format, chain CA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain FA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Z [auth F] MOL2 format, chain X [auth F] MOL2 format, chain U [auth E] MOL2 format, chain T [auth D] MOL2 format, chain AA [auth G] mmCIF format, chain CA [auth G] mmCIF format, chain EA [auth H] mmCIF format, chain FA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth D] mmCIF format, chain W [auth E] mmCIF format, chain Z [auth F] mmCIF format, chain X [auth F] mmCIF format, chain U [auth E] mmCIF format, chain T [auth D] mmCIF format, chain AA [auth G]	AA [auth G] CA [auth G] EA [auth H] FA [auth H] I [auth A] AA [auth G], CA [auth G], EA [auth H], FA [auth H], I [auth A], K [auth A], L [auth B], N [auth B], O [auth C], Q [auth C], R [auth D], T [auth D], U [auth E], W [auth E], X [auth F], Z [auth F]	INOSINIC ACID C₁₀ H₁₃ N₄ O₈ P GRSZFWQUAKGDAV-KQYNXXCUSA-N		Interactions Focus chain AA [auth G] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain FA [auth H] Focus chain I [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain T [auth D] Focus chain U [auth E] Focus chain W [auth E] Focus chain X [auth F] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth G] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain FA [auth H] Focus chain I [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain T [auth D] Focus chain U [auth E] Focus chain W [auth E] Focus chain X [auth F] Focus chain Z [auth F]