SAXSdb — 4km2

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

Dihydrofolate reductase

Mycobacterium tuberculosis

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	ATR 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE × 1 TOP TRIMETHOPRIM × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.05M KCl, 0.01M MgCl2, 15% PEG 6000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.40 Å R-free 0.201
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–159	Not recorded	ATR 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE × 1 TOP TRIMETHOPRIM × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.05M KCl, 0.01M MgCl2, 15% PEG 6000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.40 Å R-free 0.201

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.

Other PDB	Difference from Current Entry 4KM2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DF7 DIHYDROFOLATE REDUCTASE OF MYCOBACTERIUM TUBERCULOSIS COMPLEXED WITH NADPH AND METHOTREXATE Deposited 1999-11-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–159（159 aa）	Not recorded	SO4 SULFATE ION × 1 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 MTX METHOTREXATE × 1 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；277 K；AMMONIUM SULFATE, SODIUM ACETATE, GLYCEROL, NADPH, METHOTREXATE, POTASSIUM PHOSPHATE, DTT, POTASSIUM CHLORIDE, pH 4.5, VAPOR DIFFUSION, temperature 277K	Resolution 1.70 Å R-free 0.246
1DG5 DIHYDROFOLATE REDUCTASE OF MYCOBACTERIUM TUBERCULOSIS COMPLEXED WITH NADPH AND TRIMETHOPRIM Deposited 1999-11-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–159（159 aa）	Not recorded	NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 TOP TRIMETHOPRIM × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；277 K；AMMONIUM SULFATE, SODIUM ACETATE, GLYCEROL, NADPH, TRIMETHOPRIM, POTASSIUM PHOSPHATE, DTT, POTASSIUM CHLORIDE, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.243
1DG7 DIHYDROFOLATE REDUCTASE OF MYCOBACTERIUM TUBERCULOSIS COMPLEXED WITH NADPH AND 4-BROMO WR99210 Deposited 1999-11-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–159（159 aa）	Not recorded	WRB 1-[3-(4-BROMO-PHENOXY)-PROPOXY]-6,6-DIMETHYL-1.6-DIHYDRO-[1,3,5]TRIAZINE-2,4-DIAMINE × 1 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；277 K；AMMONIUM SULFATE, SODIUM ACETATE, GLYCEROL, NADPH, BROMO-WR99210, POTASSIUM PHOSPHATE, DTT, POTASSIUM CHLORIDE, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.80 Å R-free 0.246
1DG8 DIHYDROFOLATE REDUCTASE OF MYCOBACTERIUM TUBERCULOSIS COMPLEXED WITH NADPH Deposited 1999-11-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–159（159 aa）	Not recorded	NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；277 K；AMMONIUM SULFATE, SODIUM ACETATE, GLYCEROL, NADPH, POTASSIUM PHOSPHATE, DTT, POTASSIUM CHLORIDE, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.244
2CIG Dihydrofolate reductase from Mycobacterium tuberculosis inhibited by the acyclic 4R isomer of INH-NADP a derivative of the prodrug isoniazid. Deposited 2006-03-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–159（159 aa）	Not recorded	1DG (4R)-ISONICOTINIC-ACETYL-NICOTINAMIDE-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；1.6 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE, PH 4.6, 10 % GLYCEROL	Resolution 1.90 Å R-free 0.212
4KL9 Crystal structure of dihydrofolate reductase from Mycobacterium tuberculosis in the space group C2 Deposited 2013-05-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–159（159 aa）	Not recorded	NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；Mes, PEGMME 2000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.39 Å R-free 0.202
4KLX Crystal structure of dihydrofolate reductase from Mycobacterium tuberculosis in an open conformation. Deposited 2013-05-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–159（159 aa）	Not recorded	ATR 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE × 1 ETE 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；8% PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.23 Å R-free 0.244
4KLX Crystal structure of dihydrofolate reductase from Mycobacterium tuberculosis in an open conformation. Deposited 2013-05-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–159（159 aa）	Not recorded	ATR 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；8% PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.23 Å R-free 0.244
4KM0 Crystal structure of dihydrofolate reductase from Mycobacterium tuberculosis in complex with pyrimethamine Deposited 2013-05-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–159（159 aa）	Not recorded	CP6 5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMIDINE-2,4-DIAMINE × 1 ATR 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；8% PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.30 Å R-free 0.210
4KM0 Crystal structure of dihydrofolate reductase from Mycobacterium tuberculosis in complex with pyrimethamine Deposited 2013-05-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–159（159 aa）	Not recorded	CP6 5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMIDINE-2,4-DIAMINE × 1 ATR 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；8% PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.30 Å R-free 0.210
4KNE Crystal structure of dihydrofolate reductase from Mycobacterium tuberculosis in complex with cycloguanil Deposited 2013-05-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–159（159 aa）	Not recorded	1CY 1-(4-chlorophenyl)-6,6-dimethyl-1,6-dihydro-1,3,5-triazine-2,4-diamine × 1 ATR 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；8% PEG 4000, pH 7.0, VAPOR DIFFUSION, SITTING DROP	Resolution 2.00 Å R-free 0.270
4KNE Crystal structure of dihydrofolate reductase from Mycobacterium tuberculosis in complex with cycloguanil Deposited 2013-05-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–159（159 aa）	Not recorded	1CY 1-(4-chlorophenyl)-6,6-dimethyl-1,6-dihydro-1,3,5-triazine-2,4-diamine × 1 ATR 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；8% PEG 4000, pH 7.0, VAPOR DIFFUSION, SITTING DROP	Resolution 2.00 Å R-free 0.270
4M2X Mycobacterium tuberculosis dihydrofolate reductase complexed with trimetrexate (TMQ) Deposited 2013-08-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–159（159 aa）	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
4M2X Mycobacterium tuberculosis dihydrofolate reductase complexed with trimetrexate (TMQ) Deposited 2013-08-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–159（159 aa）	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
4M2X Mycobacterium tuberculosis dihydrofolate reductase complexed with trimetrexate (TMQ) Deposited 2013-08-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 1–159（159 aa）	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
4M2X Mycobacterium tuberculosis dihydrofolate reductase complexed with trimetrexate (TMQ) Deposited 2013-08-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 1–159（159 aa）	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

10 other PDB entries and 16 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 21–179； UniProt 1–159 Author chain B； PDBConstruct 21–179； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4km2
Deposition date deposition_date	2013-05-07
Structure title title	Crystal structure of Dihydrofolate reductase from Mycobacterium tuberculosis in an open conformation in complex with trimethoprim
Keywords keywords	reductase, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	23.89 Å
Radius of gyration Rg (electron density) rg_electron	22.84 Å
Forward intensity I(0) i0	25562500.00
Molecular weight molecular_weight	36873.0 kDa
Excluded volume excluded_volume	45389 Å³
Envelope volume envelope_volume	56662 Å³
Hydration-shell volume shell_volume	21065 Å³
Envelope diameter envelope_diameter	77.2 Å
Shell Rg shell_rg	29.14 Å
Envelope Rg envelope_rg	22.65 Å
Shape Rg shape_rg	22.80 Å
Total Rg total_rg	23.72 Å
Total atoms total_atoms	2592
Residues n_residues	318
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	74.9 Å
Rg (real space) rg_real	23.87 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	2.5560e+07
I(0) uncertainty (real space) i0_real_error	3.6880e+05
Rg (reciprocal space) rg_reciprocal	23.87 Å
I(0) (reciprocal space) i0_reciprocal	25560000.0000
Solution quality estimate total_estimate	0.9112
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.6 Å
Skewness Skewness skewness	0.246
Kurtosis Kurtosis kurtosis	-0.625
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3717000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.956; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.993

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Dihydrofolate reductase
Molecular weight formula_weight	19832.4 kDa
EC 编号 ec_number	1.5.1.3
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3242

MGSSHHHHHHSSGLVPRGSHMVGLIWAQATSGVIGRGGDIPWRLPEDQAHFREITMGHTIVMGRRTWDSLPAKVRPLPGRRNVVLSRQADFMASGAEVVGSLEEALTSPETWVIGGGQVYALALPYATRCEVTEVDIGLPREAGDALAPVLDETWRGETGEWRFSRSGLRYRLYSYHRS

来源 Source

来源生物 organism	Mycobacterium tuberculosis
NCBI Class编号 ncbi_taxonomy_id	1773
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	TRIMETHOPRIM
Molecular weight formula_weight	290.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	609

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4km2a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.71 — Dihydrofolate reductase-like
Superfamily Superfamily superfamily	c.71.1 — Dihydrofolate reductase-like
Family Family family	c.71.1.0 — automated matches

Domain ID domain_id	d4km2b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.71 — Dihydrofolate reductase-like
Superfamily Superfamily superfamily	c.71.1 — Dihydrofolate reductase-like
Family Family family	c.71.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	4km2A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	430 — Dihydrofolate Reductase, subunit A
Homologous superfamily homologous superfamily	10 — Dihydrofolate Reductase, subunit A

Domain ID domain_id	4km2B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	430 — Dihydrofolate Reductase, subunit A
Homologous superfamily homologous superfamily	10 — Dihydrofolate Reductase, subunit A

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8. Citations (1)

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Unit-cell length a length_a	64.160 Å
Unit-cell length b length_b	65.280 Å
Unit-cell length c length_c	79.750 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	20.990 Å
R factor r_factor	0.1437
R_work r_work	0.1406
R_free r_free	0.2008

fit	/app/data/saxs_computation/km/4km2/4km2.fit
pddf	/app/data/pr_computation/km/4km2/4km2.pr.out
profile	/app/data/saxs_computation/km/4km2/4km2.dat

Crystal structure of Dihydrofolate reductase from Mycobacterium tuberculosis in an open conformation in complex with trimethoprim

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

Dihydrofolate reductase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction