21GR | pdb_000021gr

DPR epimerase complex, PMD-bound state

PDB DOI: https://doi.org/10.2210/pdb21GR/pdb
EM Map EMD-67659: EMDB EMDataResource

Classification: ISOMERASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Mycolicibacterium smegmatis MC2 155
Mutation(s): No

Deposited: 2025-12-11 Released: 2026-09-02
Deposition Author(s): Wu, F., Gao, S., Rao, Z., Zhang, L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.73 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 21GR

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

Literature

DPR epimerase complex, PMD-bound state

Wu, F., Gao, S., Rao, Z., Zhang, L.

To be published.

Macromolecule Content

Total Structure Weight: 159.07 kDa
Atom Count: 11,040
Modeled Residue Count: 1,410
Deposited Residue Count: 1,430
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Decaprenylphosphoryl-2-keto-beta-D-erythro-pentose reductase	A [auth C], C [auth D]	254	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: dprE2, Rv3791, MTCY13D12.25 EC: 1.1.1.333
UniProt
Find proteins for P9WGS9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGS9 Go to UniProtKB: P9WGS9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WGS9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Decaprenylphosphoryl-beta-D-ribose oxidase	B, D [auth A]	461	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: dprE1, Rv3790 EC: 1.1.98.3
UniProt
Find proteins for P9WJF1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WJF1 Go to UniProtKB: P9WJF1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WJF1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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 J [auth A] SDF format, chain G [auth B] MOL2 format, chain J [auth A] MOL2 format, chain G [auth B] mmCIF format, chain J [auth A] mmCIF format, chain G [auth B]	G [auth B], J [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain G [auth B] Focus chain J [auth A] Interactions & Density Focus chain G [auth B] Focus chain J [auth A]
NAI (Subject of Investigation/LOI) Query on NAI Download:Ideal Coordinates CCD File SDF format, chain I [auth D] SDF format, chain F [auth C] MOL2 format, chain I [auth D] MOL2 format, chain F [auth C] mmCIF format, chain I [auth D] mmCIF format, chain F [auth C]	F [auth C], I [auth D]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain F [auth C] Focus chain I [auth D] Interactions & Density Focus chain F [auth C] Focus chain I [auth D]
A1L5K( Subject of Investigation/LOI) Query on A1L5K Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain E [auth C] MOL2 format, chain H [auth D] MOL2 format, chain E [auth C] mmCIF format, chain H [auth D] mmCIF format, chain E [auth C]	E [auth C], H [auth D]	pretomanid C₁₄ H₁₃ F₃ N₃ O₅ WMTOTWDJQLQWOG-NSHDSACASA-N		Interactions Focus chain E [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.73 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-02

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32394011

Revision History (Full details and data files)

Version 1.0: 2026-09-02
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.