9HG1 | pdb_00009hg1

Crystal structure of M. smegmatis GMP reductase in complex with GMP and ATP.

PDB DOI: https://doi.org/10.2210/pdb9HG1/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., Klima, M., Pichova, I.
Funding Organization(s): European Union (EU)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.230 (Depositor), 0.229 (DCC)
R-Value Work:
0.200 (Depositor), 0.200 (DCC)
R-Value Observed:
0.201 (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: 842.45 kDa
Atom Count: 57,130
Modeled Residue Count: 7,568
Deposited Residue Count: 7,936
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, I, J, K, L, M, N, O, P	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
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain W [auth D] SDF format, chain VA [auth P] SDF format, chain U [auth C] SDF format, chain TA [auth O] SDF format, chain S [auth B] SDF format, chain RA [auth N] SDF format, chain Q [auth A] SDF format, chain PA [auth M] SDF format, chain NA [auth L] SDF format, chain KA [auth K] SDF format, chain IA [auth J] SDF format, chain GA [auth I] SDF format, chain EA [auth H] SDF format, chain CA [auth G] SDF format, chain AA [auth F] MOL2 format, chain Y [auth E] MOL2 format, chain W [auth D] MOL2 format, chain VA [auth P] MOL2 format, chain U [auth C] MOL2 format, chain TA [auth O] MOL2 format, chain S [auth B] MOL2 format, chain RA [auth N] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth M] MOL2 format, chain NA [auth L] MOL2 format, chain KA [auth K] MOL2 format, chain IA [auth J] MOL2 format, chain GA [auth I] MOL2 format, chain EA [auth H] MOL2 format, chain CA [auth G] MOL2 format, chain AA [auth F] mmCIF format, chain Y [auth E] mmCIF format, chain W [auth D] mmCIF format, chain VA [auth P] mmCIF format, chain U [auth C] mmCIF format, chain TA [auth O] mmCIF format, chain S [auth B] mmCIF format, chain RA [auth N] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth M] mmCIF format, chain NA [auth L] mmCIF format, chain KA [auth K] mmCIF format, chain IA [auth J] mmCIF format, chain GA [auth I] mmCIF format, chain EA [auth H] mmCIF format, chain CA [auth G] mmCIF format, chain AA [auth F]	AA [auth F] CA [auth G] EA [auth H] GA [auth I] IA [auth J] AA [auth F], CA [auth G], EA [auth H], GA [auth I], IA [auth J], KA [auth K], NA [auth L], PA [auth M], Q [auth A], RA [auth N], S [auth B], TA [auth O], U [auth C], VA [auth P], W [auth D], Y [auth E]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain AA [auth F] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain GA [auth I] Focus chain IA [auth J] Focus chain KA [auth K] Focus chain NA [auth L] Focus chain PA [auth M] Focus chain Q [auth A] Focus chain RA [auth N] Focus chain S [auth B] Focus chain TA [auth O] Focus chain U [auth C] Focus chain VA [auth P] Focus chain W [auth D] Focus chain Y [auth E] Interactions & Density Focus chain AA [auth F] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain GA [auth I] Focus chain IA [auth J] Focus chain KA [auth K] Focus chain NA [auth L] Focus chain PA [auth M] Focus chain Q [auth A] Focus chain RA [auth N] Focus chain S [auth B] Focus chain TA [auth O] Focus chain U [auth C] Focus chain VA [auth P] Focus chain W [auth D] Focus chain Y [auth E]
5GP (Subject of Investigation/LOI) Query on 5GP Download Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain X [auth D] SDF format, chain V [auth C] SDF format, chain UA [auth P] SDF format, chain T [auth B] SDF format, chain SA [auth O] SDF format, chain R [auth A] SDF format, chain QA [auth N] SDF format, chain OA [auth M] SDF format, chain MA [auth L] SDF format, chain LA [auth K] SDF format, chain JA [auth J] SDF format, chain HA [auth I] SDF format, chain FA [auth H] SDF format, chain DA [auth G] SDF format, chain BA [auth F] MOL2 format, chain Z [auth E] MOL2 format, chain X [auth D] MOL2 format, chain V [auth C] MOL2 format, chain UA [auth P] MOL2 format, chain T [auth B] MOL2 format, chain SA [auth O] MOL2 format, chain R [auth A] MOL2 format, chain QA [auth N] MOL2 format, chain OA [auth M] MOL2 format, chain MA [auth L] MOL2 format, chain LA [auth K] MOL2 format, chain JA [auth J] MOL2 format, chain HA [auth I] MOL2 format, chain FA [auth H] MOL2 format, chain DA [auth G] MOL2 format, chain BA [auth F] mmCIF format, chain Z [auth E] mmCIF format, chain X [auth D] mmCIF format, chain V [auth C] mmCIF format, chain UA [auth P] mmCIF format, chain T [auth B] mmCIF format, chain SA [auth O] mmCIF format, chain R [auth A] mmCIF format, chain QA [auth N] mmCIF format, chain OA [auth M] mmCIF format, chain MA [auth L] mmCIF format, chain LA [auth K] mmCIF format, chain JA [auth J] mmCIF format, chain HA [auth I] mmCIF format, chain FA [auth H] mmCIF format, chain DA [auth G] mmCIF format, chain BA [auth F]	BA [auth F] DA [auth G] FA [auth H] HA [auth I] JA [auth J] BA [auth F], DA [auth G], FA [auth H], HA [auth I], JA [auth J], LA [auth K], MA [auth L], OA [auth M], QA [auth N], R [auth A], SA [auth O], T [auth B], UA [auth P], V [auth C], X [auth D], Z [auth E]	GUANOSINE-5'-MONOPHOSPHATE C₁₀ H₁₄ N₅ O₈ P RQFCJASXJCIDSX-UUOKFMHZSA-N		Interactions Focus chain BA [auth F] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain HA [auth I] Focus chain JA [auth J] Focus chain LA [auth K] Focus chain MA [auth L] Focus chain OA [auth M] Focus chain QA [auth N] Focus chain R [auth A] Focus chain SA [auth O] Focus chain T [auth B] Focus chain UA [auth P] Focus chain V [auth C] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain BA [auth F] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain HA [auth I] Focus chain JA [auth J] Focus chain LA [auth K] Focus chain MA [auth L] Focus chain OA [auth M] Focus chain QA [auth N] Focus chain R [auth A] Focus chain SA [auth O] Focus chain T [auth B] Focus chain UA [auth P] Focus chain V [auth C] Focus chain X [auth D] Focus chain Z [auth E]