4m2x

Mycobacterium tuberculosis dihydrofolate reductase complexed with trimetrexate (TMQ)

Method: X-RAY DIFFRACTION Dmax: 108.0 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Dihydrofolate reductase

Mycobacterium tuberculosis

UniProt P0A546

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1–159 Not recorded NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 TMQ TRIMETREXATE × 1 ACT ACETATE ION × 6 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.6;289 K;15% PEG 6000, 100 mM sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K Resolution 2.26 Å R-free 0.261
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 1–159 Not recorded NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 TMQ TRIMETREXATE × 1 ACT ACETATE ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.6;289 K;15% PEG 6000, 100 mM sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K Resolution 2.26 Å R-free 0.261
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain E; UniProt 1–159 Not recorded NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 TMQ TRIMETREXATE × 1 ACT ACETATE ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.6;289 K;15% PEG 6000, 100 mM sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K Resolution 2.26 Å R-free 0.261
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain G; UniProt 1–159 Not recorded NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 TMQ TRIMETREXATE × 1 ACT ACETATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.6;289 K;15% PEG 6000, 100 mM sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K Resolution 2.26 Å R-free 0.261

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

10 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DYR_MYCTU
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–162; UniProt 1–159 Author chain C; PDBConstruct 4–162; UniProt 1–159 Author chain E; PDBConstruct 4–162; UniProt 1–159 Author chain G; PDBConstruct 4–162; UniProt 1–159

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 4m2x

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4m2x
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id4m2x
Deposition date deposition_date2013-08-05
Structure title titleMycobacterium tuberculosis dihydrofolate reductase complexed with trimetrexate (TMQ)
Keywords keywords;Structural Genomics, TB Structural Genomics Consortium, TBSGC, reductase, NADPH binding, Hydride transfer, OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex ;; OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier34.23
Radius of gyration Rg (electron density) rg_electron33.82
Forward intensity I(0) i0101037000.00
Molecular weight molecular_weight76414.0 kDa
Excluded volume excluded_volume93938 ų
Envelope volume envelope_volume125020 ų
Hydration-shell volume shell_volume32116 ų
Envelope diameter envelope_diameter109.1
Shell Rg shell_rg39.04
Envelope Rg envelope_rg32.98
Shape Rg shape_rg33.80
Total Rg total_rg34.26
Total atoms total_atoms5369
Residues n_residues636
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax108.0
Rg (real space) rg_real34.24
Rg uncertainty (real space) rg_real_error0.98
I(0) (real space) i0_real1.0100e+08
I(0) uncertainty (real space) i0_real_error1.8480e+06
Rg (reciprocal space) rg_reciprocal34.24
I(0) (reciprocal space) i0_reciprocal101000000.0000
Solution quality estimate total_estimate0.8874
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary47.0
Skewness Skewness skewness0.198
Kurtosis Kurtosis kurtosis-0.693
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14240000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.938; Smooth: 0.809

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd4m2xa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.71 — Dihydrofolate reductase-like
Superfamily Superfamily superfamilyc.71.1 — Dihydrofolate reductase-like
Family Family familyc.71.1.0 — automated matches
Domain ID domain_idd4m2xc_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.71 — Dihydrofolate reductase-like
Superfamily Superfamily superfamilyc.71.1 — Dihydrofolate reductase-like
Family Family familyc.71.1.0 — automated matches
Domain ID domain_idd4m2xe_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.71 — Dihydrofolate reductase-like
Superfamily Superfamily superfamilyc.71.1 — Dihydrofolate reductase-like
Family Family familyc.71.1.0 — automated matches
Domain ID domain_idd4m2xg_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.71 — Dihydrofolate reductase-like
Superfamily Superfamily superfamilyc.71.1 — Dihydrofolate reductase-like
Family Family familyc.71.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id4m2xA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology430 — Dihydrofolate Reductase, subunit A
Homologous superfamily homologous superfamily10 — Dihydrofolate Reductase, subunit A
Domain ID domain_id4m2xC00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology430 — Dihydrofolate Reductase, subunit A
Homologous superfamily homologous superfamily10 — Dihydrofolate Reductase, subunit A
Domain ID domain_id4m2xE00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology430 — Dihydrofolate Reductase, subunit A
Homologous superfamily homologous superfamily10 — Dihydrofolate Reductase, subunit A
Domain ID domain_id4m2xG00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology430 — Dihydrofolate Reductase, subunit A
Homologous superfamily homologous superfamily10 — Dihydrofolate Reductase, subunit A

8. Citations (1)

9. Files and Curves (10)