9M1V | pdb_00009m1v

Crystal structure of N-terminal domain of hypothetical protein Rv1421 from Mycobacterium tuberculosis H37Rv in complex with uridine diphosphate N-acetyl glucosamine

• PDB DOI: https://doi.org/10.2210/pdb9M1V/pdb

• Classification: HYDROLASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-02-26 Released: 2025-09-03 
• Deposition Author(s): Lee, K.S., Park, J.
• Funding Organization(s): National Research Foundation (NRF, Korea)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.215 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: in silico

Literature

Structure-based biochemical properties of N-terminal domain of hypothetical protein Rv1421 from Mycobacterium tuberculosis H37Rv in complex with uridine diphosphate N-acetyl glucosamine

Lee, K.S., Park, J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 77.52 kDa 
• Atom Count: 5,195 
• Modeled Residue Count: 628 
• Deposited Residue Count: 696 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleotide-binding protein Rv1421	A, B, C, D	174	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: Rv1421, MTCY21B4.39
UniProt
Find proteins for P9WFQ3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFQ3  Go to UniProtKB:  P9WFQ3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UD1 (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], I [auth D]	URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE C17 H27 N3 O17 P2 LFTYTUAZOPRMMI-CFRASDGPSA-N
P6G (Subject of Investigation/LOI)	H [auth C]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.215 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.305	α = 90
b = 116.944	β = 93.076
c = 61.646	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Lee, K.S., Park, J.

---

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2021R1F1A1047349

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release