6vcj

Crystal structure of hsDHFR in complex with NADP+, DAP, and R-naproxen

Method: X-RAY DIFFRACTION Dmax: 105.4 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 1–187 Not recorded LG3 PYRIMIDINE-2,4-DIAMINE × 1 NPX (2R)-2-(6-methoxynaphthalen-2-yl)propanoic acid × 1 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 FOL FOLIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.4;293 K;Protein solution: 9mg/ml in 50mM NaCl, 10mM Tris, 5mM NADP+, 10mM 2,4-diaminopyrimidine, 20mM R-Naproxen Mother Liquor: 20% PEG 20,000 Resolution 2.34 Å R-free 0.238
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–187 Not recorded LG3 PYRIMIDINE-2,4-DIAMINE × 1 NPX (2R)-2-(6-methoxynaphthalen-2-yl)propanoic acid × 1 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 FOL FOLIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.4;293 K;Protein solution: 9mg/ml in 50mM NaCl, 10mM Tris, 5mM NADP+, 10mM 2,4-diaminopyrimidine, 20mM R-Naproxen Mother Liquor: 20% PEG 20,000 Resolution 2.34 Å R-free 0.238
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 1–187 Not recorded LG3 PYRIMIDINE-2,4-DIAMINE × 1 NPX (2R)-2-(6-methoxynaphthalen-2-yl)propanoic acid × 1 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 FOL FOLIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.4;293 K;Protein solution: 9mg/ml in 50mM NaCl, 10mM Tris, 5mM NADP+, 10mM 2,4-diaminopyrimidine, 20mM R-Naproxen Mother Liquor: 20% PEG 20,000 Resolution 2.34 Å R-free 0.238
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 1–187 Not recorded LG3 PYRIMIDINE-2,4-DIAMINE × 1 NPX (2R)-2-(6-methoxynaphthalen-2-yl)propanoic acid × 1 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 FOL FOLIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.4;293 K;Protein solution: 9mg/ml in 50mM NaCl, 10mM Tris, 5mM NADP+, 10mM 2,4-diaminopyrimidine, 20mM R-Naproxen Mother Liquor: 20% PEG 20,000 Resolution 2.34 Å R-free 0.238

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 102 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 2–188; UniProt 1–187 Author chain B; PDBConstruct 2–188; UniProt 1–187 Author chain C; PDBConstruct 2–188; UniProt 1–187 Author chain D; PDBConstruct 2–188; UniProt 1–187

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 6vcj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6vcj
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6vcj
Deposition date deposition_date2019-12-21
Structure title titleCrystal structure of hsDHFR in complex with NADP+, DAP, and R-naproxen
Keywords keywordsNADP+, 2, 4-diaminopyridine, R-naproxen, inhibitor, complex, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier32.15
Radius of gyration Rg (electron density) rg_electron31.57
Forward intensity I(0) i0115218000.00
Molecular weight molecular_weight85616.0 kDa
Excluded volume excluded_volume107240 ų
Envelope volume envelope_volume135800 ų
Hydration-shell volume shell_volume36782 ų
Envelope diameter envelope_diameter110.1
Shell Rg shell_rg37.71
Envelope Rg envelope_rg31.18
Shape Rg shape_rg31.58
Total Rg total_rg32.08
Total atoms total_atoms6026
Residues n_residues737
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 dmax105.4
Rg (real space) rg_real32.15
Rg uncertainty (real space) rg_real_error0.71
I(0) (real space) i0_real1.1520e+08
I(0) uncertainty (real space) i0_real_error2.0270e+06
Rg (reciprocal space) rg_reciprocal32.15
I(0) (reciprocal space) i0_reciprocal115200000.0000
Solution quality estimate total_estimate0.8811
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary45.2
Skewness Skewness skewness0.295
Kurtosis Kurtosis kurtosis-0.364
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha68660000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.877; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.833

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd6vcja_
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_idd6vcjb_
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_idd6vcjc_
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_idd6vcjd_
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

8. Citations (1)

9. Files and Curves (10)