4OL9 | pdb_00004ol9

Crystal Structure of putative 2-dehydropantoate 2-reductase PanE from Mycobacterium tuberculosis complexed with NADP and oxamate

• PDB DOI: https://doi.org/10.2210/pdb4OL9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-01-23 Released: 2014-02-26 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.176 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of putative 2-dehydropantoate 2-reductase PanE from Mycobacterium tuberculosis complexed with NADP and oxamate

Dranow, D.M., Wernimont, A.K., Abendroth, A., Pierce, P.G., Bullen, J., Edwards, T.E., Lorimer, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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)

Macromolecule Content 

• Total Structure Weight: 33.23 kDa 
• Atom Count: 2,552 
• Modeled Residue Count: 297 
• Deposited Residue Count: 304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative 2-dehydropantoate 2-reductase	A	304	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: Rv2573, MT2649, MTCY227.28c EC: 1.1.1.169
UniProt
Find proteins for P9WIL1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WIL1  Go to UniProtKB:  P9WIL1

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
OXM	C [auth A]	OXAMIC ACID C2 H3 N O3 SOWBFZRMHSNYGE-UHFFFAOYSA-N
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.176 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34OL9

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.59	α = 90
b = 108.52	β = 90
c = 47.29	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-26 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2014-02-26
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2025-10-22
  Changes: Database references, Structure summary