SAXSdb — 4ixe

▼

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

Dihydrofolate reductase

Pneumocystis carinii

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 D； UniProt 1–206	Not recorded	IXE N~6~-methyl-N~6~-(3,4,5-trifluorophenyl)pyrido[2,3-d]pyrimidine-2,4,6-triamine × 1 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；287 K；0.1 HEPS, 25% PEG2000 MME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K	Resolution 1.54 Å R-free 0.220

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 4IXE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CD2 LIGAND INDUCED CONFORMATIONAL CHANGES IN THE CRYSTAL STRUCTURES OF PNEUMOCYSTIS CARINII DIHYDROFOLATE REDUCTASE COMPLEXES WITH FOLATE AND NADP+ Deposited 1999-03-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–206（206 aa）	Not recorded	NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 FOL FOLIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；10 ML PROTEIN, 1 MICROLITER 50MM MES, PH 6.5, 100MM KCL, 9 ML 50%(W/W)PEG 2K., pH 6.00	Resolution 2.20 Å
1DAJ COMPARISON OF TERNARY COMPLEXES OF PNEUMOCYSTIS CARINII AND WILD TYPE HUMAN DIHYDROFOLATE REDUCTASE WITH COENZYME NADPH AND A NOVEL CLASSICAL ANTITUMOR FURO[2,3D]PYRIMIDINE ANTIFOLATE Deposited 1997-07-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–206（206 aa）	Not recorded	NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 MOT N-[4-[(2,4-DIAMINOFURO[2,3D]PYRIMIDIN-5-YL)METHYL]METHYLAMINO]-BENZOYL]-L-GLUTAMATE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1DYR THE STRUCTURE OF PNEUMOCYSTIS CARINII DIHYDROFOLATE REDUCTASE TO 1.9 ANGSTROMS RESOLUTION Deposited 1994-09-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–206（206 aa）	Not recorded	NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 TOP TRIMETHOPRIM × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.86 Å
1E26 Design, Synthesis and X-ray Crystal Structure of a Potent Dual Inhibitor of Thymidylate Synthase and Dihydrofolate Reductase as an Antitumor Agent. Deposited 2000-05-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–206（206 aa）	Not recorded	NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 GPB N-[4-[2-(2-AMINO-4-METHYL-7H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYL]GLUTAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 6；PROTEIN SOLUTION: WASHED AND CONCENTRATED 4 TUBES PCDHFR USING A CENTRICON 10 50 MM MES, 100MM KCL, B-NADPH, PH 6.0, A280/340 RATIO OF 24. WASHED WITH 50MM MES, 100MM KCL, PH 6.0, WASHED WITH 50MM MES, 100MM KCL, PH 6.0 TO A CONCENTRATION OF 6.5 MG/ML. RESERVOIR SOLUTION: 50% PEG2000MME, 50MM MES, 100MM, PH 6.0 SET UP MICROBATCH POLYTHERMAL GRADIENT EXPERIMENTS IN MICROPETS. DROPS WERE COMPOSED OF: 2.5 MICROLITERS PROTEIN SOLUTION 2.0 MICROLITERS PROTEIN SOLUTION 0.5 MICROLITERS 50MM MES, 100MM KCL, PH 6.0. MICROPETS WERE LEFT TO EQUILIBRATE ON THE POLYTHERMAL GRADIENT.	Resolution 2.00 Å R-free 0.297
1KLK CRYSTAL STRUCTURE OF PNEUMOCYSTIS CARINII DIHYDROFOLATE REDUCTASE TERNARY COMPLEX WITH PT653 AND NADPH Deposited 2001-12-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–206（206 aa）	Not recorded	PMD [N-(2,4-DIAMINOPTERIDIN-6-YL)-METHYL]-DIBENZ[B,F]AZEPINE × 1 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；PEG 2000MME, KCl, MES, pH 6.0, VAPOR DIFFUSION, temperature 298K	Resolution 2.30 Å R-free 0.289
1LY3 ANALYSIS OF QUINAZOLINE AND PYRIDOPYRIMIDINE N9-C10 REVERSED BRIDGE ANTIFOLATES IN COMPLEX WITH NADP+ AND PNEUMOCYSTIS CARINII DIHYDROFOLATE REDUCTASE Deposited 2002-06-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–206（206 aa）	Not recorded	NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 COG 2,4-DIAMINO-6-[N-(2',5'-DIMETHOXYBENZYL)-N-METHYLAMINO]QUINAZOLINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；Peg 2000, MES/KCl, KCl, pH 6, VAPOR DIFFUSION, temperature 298K	Resolution 1.90 Å
1LY4 Analysis of quinazoline and PYRIDO[2,3D]PYRIMIDINE N9-C10 reversed bridge antifolates in complex with NADP+ and Pneumocystis carinii dihydrofolate reductase Deposited 2002-06-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–206（206 aa）	Not recorded	NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 COQ 2,4-DIAMINO-6-[N-(3',5'-DIMETHOXYBENZYL)-N-METHYLAMINO]PYRIDO[2,3-D]PYRIMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；MES/KCl, PEG 2000, pH 6.0, VAPOR DIFFUSION, temperature 298K	Resolution 2.10 Å
1S3Y Structure Determination of Tetrahydroquinazoline Antifolates in Complex with Human and Pneumocystis carinii Dihydrofolate Reductase: Correlations of Enzyme Selectivity and Stereochemistry Deposited 2004-01-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–206（206 aa）	Not recorded	NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 TQT 6-(OCTAHYDRO-1H-INDOL-1-YLMETHYL)DECAHYDROQUINAZOLINE-2,4-DIAMINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions thermal gradient；pH 6；298 K；50 mM MES, 100 mM KCl, pH 6.0, thermal gradient, temperature 298K	Resolution 2.25 Å R-free 0.289
1VJ3 STRUCTURAL STUDIES ON BIO-ACTIVE COMPOUNDS. CRYSTAL STRUCTURE AND MOLECULAR MODELING STUDIES ON THE PNEUMOCYSTIS CARINII DIHYDROFOLATE REDUCTASE COFACTOR COMPLEX WITH TAB, A HIGHLY SELECTIVE ANTIFOLATE. Deposited 2004-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–206（205 aa）	Not recorded	NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 TAB ACETIC ACID N-[2-CHLORO-5-[6-ETHYL-2,4-DIAMINO-PYRIMID-5-YL]-PHENYL]-[BENZYL-TRIAZEN-3-YL]ETHYL ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.00	Resolution 2.10 Å
2CD2 LIGAND INDUCED CONFORMATIONAL CHANGES IN THE CRYSTAL STRUCTURES OF PNEUMOCYSTIS CARINII DIHYDROFOLATE REDUCTASE COMPLEXES WITH FOLATE AND NADP+ Deposited 1999-03-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–206（206 aa）	Not recorded	NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 FOL FOLIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.00	Resolution 1.90 Å
2FZH New Insights into Dihydrofolate Reductase Interactions: Analysis of Pneumocystis carinii and Mouse DHFR Complexes with NADPH and Two Highly Potent Trimethoprim Derivatives Deposited 2006-02-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–206（206 aa）	Not recorded	NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 DH1 2,4-DIAMINO-5-[2-METHOXY-5-(4-CARBOXYBUTYLOXY)BENZYL]PYRIMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；33% PEG 2K, 46 mM MES, 100 mM KCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.295
2FZI New Insights into DHFR Interactions: Analysis of Pneumocystis carinii and Mouse DHFR Complexes with NADPH and Two Highly Potent Trimethoprim Derivatives Deposited 2006-02-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–206（206 aa）	Not recorded	NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 DH3 2,4-DIAMINO-5-[3',4'-DIMETHOXY-5'-(5-CARBOXYL-1-PENTYNYL)]BENZYL PYRIMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；33% PEG 2K, 46 mM MES, 100 mM KCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.60 Å R-free 0.317
3CD2 LIGAND INDUCED CONFORMATIONAL CHANGES IN THE CRYSTAL STRUCTURES OF PNEUMOCYSTIS CARINII DIHYDROFOLATE REDUCTASE COMPLEXES WITH FOLATE AND NADP+ Deposited 1999-03-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–206（206 aa）	Not recorded	NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 MTX METHOTREXATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 2.50 Å
3NZ6 Structural Analysis of Pneumocystis carinii and Human DHFR Complexes with NADPH and a Series of Five Potent 5-(omega-Carboxy(alkyloxy)Pyrido[2,3-d]pyrimidine Derivatives Deposited 2010-07-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 1–206（206 aa）	Not recorded	D2J 6-{3-[(2,4-diamino-5-methylpyrido[2,3-d]pyrimidin-6-yl)methyl]-4-methoxyphenoxy}hexanoic acid × 1 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；273 K；33-36% PEG 2K, 46-52 mM MES pH 6 100 mM KCL, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 2.00 Å R-free 0.287
3NZ9 Structural Analysis of Pneumocystis carinii and Human DHFR Complexes with NADPH and a Series of Five Potent 5-(omega-Carboxy(alkyloxy)Pyrido[2,3-d]pyrimidine Derivatives Deposited 2010-07-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 1–206（206 aa）	Not recorded	NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 D2K ethyl 4-{3-[(2,4-diamino-5-methylpyrido[2,3-d]pyrimidin-6-yl)methyl]-4-methoxyphenoxy}butanoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；273 K；33-336% PEG 2K, 46-52 mM MES pH 6 100 mM KCl, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 1.80 Å R-free 0.272
3NZA Structural Analysis of Pneumocystis carinii and Human DHFR Complexes with NADPH and a Series of Five Potent 5-(omega-Carboxy(alkyloxy)pyrido[2,3-d]pyrimidine Derivatives Deposited 2010-07-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 1–206（206 aa）	Not recorded	NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 D2K ethyl 4-{3-[(2,4-diamino-5-methylpyrido[2,3-d]pyrimidin-6-yl)methyl]-4-methoxyphenoxy}butanoate × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；273 K；33-36% PEG 2K, 46-52 mM MES pH 6.0, 100 mM KCl, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 1.90 Å R-free 0.282
3NZB Structural Analysis of Pneumocystis carinii and Human DHFR Complexes with NADPH and a Series of Potent 5-(omega-carboxyl(alkyloxy)pyrido[2,-d]pyrimidine Derivatives Deposited 2010-07-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 1–206（206 aa）	Not recorded	D2N ethyl 6-{3-[(2,4-diamino-5-methylpyrido[2,3-d]pyrimidin-6-yl)methyl]-4-methoxyphenoxy}hexanoate × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；273 K；33-36% PEG 2K, 46-52 mM MES, 100 mM KCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 1.45 Å R-free 0.295
3NZC Structural Analysis of Pneumocystis carinii and Human DHFR Complexes with NADPH and a Series of Five Potent 5-(omega-carboxy(alkyloxy)pyrido[2,3-d]pyridine Derivativea Deposited 2010-07-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 1–206（206 aa）	Not recorded	D2O 6-[2-methoxy-5-(2-phenylethoxy)benzyl]-5-methylpyrido[2,3-d]pyrimidine-2,4-diamine × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；273 K；30-36% PEG 2K, 46-52 mM MES, 100 mM KCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 2.00 Å R-free 0.260
3TD8 Structural Analysis of Pneumocystis carinii Dihydrofolate Reductase Complex with NADPH and 2,4-diamino-5-methyl-6-[2'-(4-carboxy-1-pentynyl)-5'-methoxybenzyl]pyrido[2,3-d]pyrimidine Deposited 2011-08-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–206（206 aa）	Not recorded	NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 D2R 6-{2-[(2,4-diamino-5-methylpyrido[2,3-d]pyrimidin-6-yl)methyl]-4-methoxyphenyl}hex-5-ynoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；273 K；33% PEG 2K, 46 mM MES, pH 6.0, 100 mM KCl, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 1.80 Å R-free 0.259
4CD2 LIGAND INDUCED CONFORMATIONAL CHANGES IN THE CRYSTAL STRUCTURES OF PNEUMOCYSTIS CARINII DIHYDROFOLATE REDUCTASE COMPLEXES WITH FOLATE AND NADP+ Deposited 1999-03-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–206（206 aa）	Not recorded	FOL FOLIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 2.00 Å
4G8Z pcDHFR K37S/F69N double mutant TMP NADPH ternary complex Deposited 2012-07-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 3–206（204 aa） Fragment：dihydrofolate reductase	Mutation：K37S and F69N	TOP TRIMETHOPRIM × 1 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；287 K；33-36% PEG 2K, 50 mM MES, pH 6.0, 100 mM KCl, VAPOR DIFFUSION, HANGING DROP, temperature 287K	Resolution 1.75 Å R-free 0.316
4IXF pcDHFR-269 F69N variant Deposited 2013-01-25	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 1–206（206 aa）	Mutation：F69N	NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 IXF N~6~-methyl-N~6~-[4-(propan-2-yl)phenyl]pyrido[2,3-d]pyrimidine-2,4,6-triamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；287 K；35% PEG 2000, 49 mM MES, 100 mM KCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K	Resolution 1.70 Å R-free 0.248
4IXG pcDHFR-268-K37S-N69F variant Deposited 2013-01-25	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 1–206（206 aa）	Mutation：K37S, F69N	NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 IXG N~6~-methyl-N~6~-phenylpyrido[2,3-d]pyrimidine-2,4,6-triamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；287 K；35% PEG2000, 49 mM MES, 100 mM KCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K	Resolution 1.70 Å R-free 0.280
4QJZ Pneumocystis carinii dihydrofolate reductase ternary complex with NADPH and the inhibitor 24, (N~6~-METHYL-N~6~-(NAPHTHALEN-1-YL)PYRIDO[2,3-D]PYRIMIDINE-2,4,6-TRIAMINE) Deposited 2014-06-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–206（206 aa） Fragment：Pneumocystis carinii dihydrofolate reductase	Not recorded	33M N~6~-methyl-N~6~-(naphthalen-1-yl)pyrido[2,3-d]pyrimidine-2,4,6-triamine × 1 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；287 K；ProComplex #11: 0.1 M HEPES, pH 7.5, 25% PEG2KMME, VAPOR DIFFUSION, HANGING DROP, temperature 287K	Resolution 1.61 Å R-free 0.245

24 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DYR_PNECA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain D； PDBConstruct 1–206； UniProt 1–206

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4ixe
Deposition date deposition_date	2013-01-25
Structure title title	pcDHFR-NADPH-270
Keywords keywords	dihydrofolate reductase inhibitor cofactor ternary complex, reductase, OXIDOREDUCTASE-Inhibitor complex; OXIDOREDUCTASE/Inhibitor
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	17.99 Å
Radius of gyration Rg (electron density) rg_electron	16.64 Å
Forward intensity I(0) i0	11149500.00
Molecular weight molecular_weight	24954.0 kDa
Excluded volume excluded_volume	31265 Å³
Envelope volume envelope_volume	35083 Å³
Hydration-shell volume shell_volume	17349 Å³
Envelope diameter envelope_diameter	56.5 Å
Shell Rg shell_rg	23.03 Å
Envelope Rg envelope_rg	17.00 Å
Shape Rg shape_rg	16.62 Å
Total Rg total_rg	17.70 Å
Total atoms total_atoms	1757
Residues n_residues	206
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

▼

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

Maximum dimension Dmax dmax	58.0 Å
Rg (real space) rg_real	17.85 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	1.1150e+07
I(0) uncertainty (real space) i0_real_error	1.2870e+05
Rg (reciprocal space) rg_reciprocal	17.87 Å
I(0) (reciprocal space) i0_reciprocal	11150000.0000
Solution quality estimate total_estimate	0.8825
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.3 Å
Skewness Skewness skewness	0.113
Kurtosis Kurtosis kurtosis	-0.391
Angular range angular_range	— – 0.4400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2467000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.828; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.998

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Dihydrofolate reductase
Molecular weight formula_weight	23918.5 kDa
EC 编号 ec_number	1.5.1.3
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D
Atom count atom_count	1871

MNQQKSLTLIVALTTSYGIGRSNSLPWKLKKEISYFKRVTSFVPTFDSFESMNVVLMGRKTWESIPLQFRPLKGRINVVITRNESLDLGNGIHSAKSLDHALELLYRTYGSESSVQINRIFVIGGAQLYKAAMDHPKLDRIMATIIYKDIHCDVFFPLKFRDKEWSSVWKKEKHSDLESWVGTKVPHGKINEDGFDYEFEMWTRDL

来源 Source

来源生物 organism	Pneumocystis carinii
NCBI Class编号 ncbi_taxonomy_id	4754
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	N~6~-methyl-N~6~-(3,4,5-trifluorophenyl)pyrido[2,3-d]pyrimidine-2,4,6-triamine
Molecular weight formula_weight	320.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Molecular weight formula_weight	745.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	114

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4ixed_
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.71.1.1 — Dihydrofolate reductases

CATH v4.4 (1 domains)

Domain ID domain_id	4ixeD00
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

▶

8. Citations (1)

▶

Unit-cell length a length_a	36.708 Å
Unit-cell length b length_b	42.719 Å
Unit-cell length c length_c	58.481 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.59 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.540 Å
Low-resolution limit resolution_low	36.640 Å
R factor r_factor	0.1793
R_work r_work	0.1770
R_free r_free	0.2202

fit	/app/data/saxs_computation/ix/4ixe/4ixe.fit
pddf	/app/data/pr_computation/ix/4ixe/4ixe.pr.out
profile	/app/data/saxs_computation/ix/4ixe/4ixe.dat

pcDHFR-NADPH-270

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