4M2X

Mycobacterium tuberculosis dihydrofolate reductase complexed with trimetrexate (TMQ)

PDB DOI: https://doi.org/10.2210/pdb4M2X/pdb

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

Deposited: 2013-08-05 Released: 2014-11-12
Deposition Author(s): Jung, H., Sacchettini, J.C., TB Structural Genomics Consortium (TBSGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free: 0.261
R-Value Work: 0.197

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Selective inhibitors for dihydrofolate reductase from mycobacterium tuberculosis

Jung, H., Sacchettini, J.C.

To be published.

Macromolecule Content

Total Structure Weight: 77.63 kDa
Atom Count: 5,467
Modelled Residue Count: 636
Deposited Residue Count: 648
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A, B [auth C], C [auth E], D [auth G]	162	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: folA, dfrA, Rv2763c, MT2833, MTV002.28c EC: 1.5.1.3
UniProt
Find proteins for P9WNX1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WNX1 Go to UniProtKB: P9WNX1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WNX1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download Ideal Coordinates CCD File SDF format, chain DA [auth G] SDF format, chain E [auth A] SDF format, chain N [auth C] SDF format, chain V [auth E] MOL2 format, chain DA [auth G] MOL2 format, chain E [auth A] MOL2 format, chain N [auth C] MOL2 format, chain V [auth E] mmCIF format, chain DA [auth G] mmCIF format, chain E [auth A] mmCIF format, chain N [auth C] mmCIF format, chain V [auth E]	DA [auth G], E [auth A], N [auth C], V [auth E]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain DA [auth G] Focus chain E [auth A] Focus chain N [auth C] Focus chain V [auth E] Interactions & Density Focus chain DA [auth G] Focus chain E [auth A] Focus chain N [auth C] Focus chain V [auth E]
TMQ Query on TMQ Download Ideal Coordinates CCD File SDF format, chain EA [auth G] SDF format, chain F [auth A] SDF format, chain O [auth C] SDF format, chain W [auth E] MOL2 format, chain EA [auth G] MOL2 format, chain F [auth A] MOL2 format, chain O [auth C] MOL2 format, chain W [auth E] mmCIF format, chain EA [auth G] mmCIF format, chain F [auth A] mmCIF format, chain O [auth C] mmCIF format, chain W [auth E]	EA [auth G], F [auth A], O [auth C], W [auth E]	TRIMETREXATE C₁₉ H₂₄ N₅ O₃ NOYPYLRCIDNJJB-UHFFFAOYSA-O		Interactions Focus chain EA [auth G] Focus chain F [auth A] Focus chain O [auth C] Focus chain W [auth E] Interactions & Density Focus chain EA [auth G] Focus chain F [auth A] Focus chain O [auth C] Focus chain W [auth E]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain CA [auth E] SDF format, chain FA [auth G] SDF format, chain G [auth A] SDF format, chain GA [auth G] SDF format, chain H [auth A] SDF format, chain HA [auth G] SDF format, chain I [auth A] SDF format, chain IA [auth G] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain X [auth E] SDF format, chain Y [auth E] SDF format, chain Z [auth E] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain FA [auth G] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth G] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth G] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E] mmCIF format, chain AA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain FA [auth G] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth G] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth G] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain X [auth E] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth E]	AA [auth E] BA [auth E] CA [auth E] FA [auth G] G [auth A] AA [auth E], BA [auth E], CA [auth E], FA [auth G], G [auth A], GA [auth G], H [auth A], HA [auth G], I [auth A], IA [auth G], J [auth A], K [auth A], L [auth A], P [auth C], Q [auth C], R [auth C], S [auth C], T [auth C], U [auth C], X [auth E], Y [auth E], Z [auth E]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain FA [auth G] Focus chain G [auth A] Focus chain GA [auth G] Focus chain H [auth A] Focus chain HA [auth G] Focus chain I [auth A] Focus chain IA [auth G] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain FA [auth G] Focus chain G [auth A] Focus chain GA [auth G] Focus chain H [auth A] Focus chain HA [auth G] Focus chain I [auth A] Focus chain IA [auth G] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free: 0.261
R-Value Work: 0.197
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.09	α = 93.48
b = 64.838	β = 94.1
c = 68.062	γ = 100.25

Software Package:

Software Name	Purpose
d*TREK	data scaling
d*TREK	data reduction
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
CrystalClear	data reduction
CrystalClear	data scaling