4keb

Human dihydrofolate reductase complexed with NADPH and 5-{3-[3-methoxy-5-(isoquin-5-yl)phenyl]but-1-yn-1-yl}6-ethylpyrimidine-2,4-diamine

Method: X-RAY DIFFRACTION Dmax: 84.5 Å Quality: GOOD

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

Dihydrofolate reductase

Homo sapiens

UniProt P00374

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 2–187 Not recorded NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 1QZ 6-ethyl-5-{(3S)-3-[3-(isoquinolin-5-yl)-5-methoxyphenyl]but-1-yn-1-yl}pyrimidine-2,4-diamine × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;277 K;0.1M Tris-HCl, 0.2-0.3M lithium sulfate, 25-32%(w/v) PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 1.45 Å R-free 0.206
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 2–187 Not recorded NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 FOL FOLIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;277 K;0.1M Tris-HCl, 0.2-0.3M lithium sulfate, 25-32%(w/v) PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 1.45 Å R-free 0.206

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.

88 other PDB entries and 104 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DYR_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–186; UniProt 2–187 Author chain B; PDBConstruct 1–186; UniProt 2–187

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 4keb

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4keb
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4keb
Deposition date deposition_date2013-04-25
Structure title titleHuman dihydrofolate reductase complexed with NADPH and 5-{3-[3-methoxy-5-(isoquin-5-yl)phenyl]but-1-yn-1-yl}6-ethylpyrimidine-2,4-diamine
Keywords keywordsOxidoreductase, 5, 6, 7, 8-tetrahydrofolate, NADP+, hydride shift, cytosol, 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_guinier25.80
Radius of gyration Rg (electron density) rg_electron25.04
Forward intensity I(0) i034029700.00
Molecular weight molecular_weight44999.0 kDa
Excluded volume excluded_volume56324 ų
Envelope volume envelope_volume68456 ų
Hydration-shell volume shell_volume23839 ų
Envelope diameter envelope_diameter88.1
Shell Rg shell_rg31.15
Envelope Rg envelope_rg25.12
Shape Rg shape_rg25.01
Total Rg total_rg25.83
Total atoms total_atoms3164
Residues n_residues372
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 dmax84.5
Rg (real space) rg_real25.93
Rg uncertainty (real space) rg_real_error0.51
I(0) (real space) i0_real3.4030e+07
I(0) uncertainty (real space) i0_real_error4.2130e+05
Rg (reciprocal space) rg_reciprocal25.89
I(0) (reciprocal space) i0_reciprocal34030000.0000
Solution quality estimate total_estimate0.8665
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.5
Skewness Skewness skewness0.438
Kurtosis Kurtosis kurtosis-0.508
Angular range angular_range— – 0.3100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11300000.0000
Real-space data points n_real_points63
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.794; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.914; Smooth: 0.965

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4keba_
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.71.1.1 — Dihydrofolate reductases
Domain ID domain_idd4kebb_
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.71.1.1 — Dihydrofolate reductases

CATH v4.4 (2 domains)

Domain ID domain_id4kebA00
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_id4kebB00
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)