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
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Ligand Structure Quality Assessment

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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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WFQ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UD1 (Subject of Investigation/LOI) Query on UD1 Download:Ideal Coordinates CCD File SDF format, chain I [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], I [auth D]	URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE C₁₇ H₂₇ N₃ O₁₇ P₂ LFTYTUAZOPRMMI-CFRASDGPSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain I [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain I [auth D]
P6G (Subject of Investigation/LOI) Query on P6G Download:Ideal Coordinates CCD File SDF format, chain H [auth C] MOL2 format, chain H [auth C] mmCIF format, chain H [auth C]	H [auth C]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Interactions & Density Focus chain H [auth C]

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-03

Deposition Author(s):

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

Revision History (Full details and data files)

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

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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.