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2qpl

Crystal structure of calf spleen purine nucleoside phosphorylase complexed to a novel purine analogue

Method: X-RAY DIFFRACTION Dmax: 61.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Purine nucleoside phosphorylase

OrganismNot specified

UniProt P55859

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 3–284 Not recorded SO4 SULFATE ION × 3 MG MAGNESIUM ION × 3 BTY 4-amino-7-methylpyrazolo[1,5-a][1,3,5]triazin-2(1H)-one × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；291 K；31-35% PEG-400 IN 100 MM HEPES OR TRIS BUFFER, PH 7.8-8.2; 100 MM MGCL2; 1% OCTYL-BETA-D-GLUCOPYRANOSIDE , pH 8.0, VAPOR DIFFUSION, temperature 291K Resolution 2.10 Å R-free 0.218

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 2QPL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A9O BOVINE PURINE NUCLEOSIDE PHOSPHORYLASE COMPLEXED WITH PHOSPHATE Deposited 1998-04-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–289（289 aa）
Not recorded PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions PROTEIN WAS CRYSTALLIZED FROM 31-35% PEG-400 IN 100 MM TRIS BUFFER, PH 7.8-8.2; 100 MM MGCL2; 1% OCTYL-BETA- D-GLUCOPYRANOSIDE
Resolution 2.00 Å
1A9P BOVINE PURINE NUCLEOSIDE PHOSPHORYLASE COMPLEXED WITH 9-DEAZAINOSINE AND PHOSPHATE Deposited 1998-04-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–289（289 aa）
Not recorded PO4 PHOSPHATE ION × 3 9DI 9-DEAZAINOSINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions PROTEIN WAS CRYSTALLIZED FROM 31-35% PEG-400 IN 100 MM HEPES OR TRIS BUFFER, PH 7.8-8.2; 100 MM MGCL2; 1% OCTYL-BETA- D-GLUCOPYRANOSIDE
Resolution 2.40 Å
1A9Q BOVINE PURINE NUCLEOSIDE PHOSPHORYLASE COMPLEXED WITH INOSINE Deposited 1998-04-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–282（282 aa）
Not recorded SO4 SULFATE ION × 3 HPA HYPOXANTHINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions PROTEIN WAS CRYSTALLIZED FROM 31-35% PEG-400 IN 100 MM HEPES BUFFER, PH 7.8-8.2; 100 MM MGCL2; 1% OCTYL-BETA- D-GLUCOPYRANOSIDE. CRYSTAL SOAKED IN ARTI- FICIAL MOTHER LIQUOR CONTAINING 7.3 MM INOSINE.
Resolution 2.00 Å
1A9R BOVINE PURINE NUCLEOSIDE PHOSPHORYLASE COMPLEXED WITH HYPOXANTHINE AND SULFATE Deposited 1998-04-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–282（282 aa）
Not recorded SO4 SULFATE ION × 3 HPA HYPOXANTHINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions PROTEIN WAS CRYSTALLIZED FROM 31-35% PEG-400 IN 100 MM HEPES OR TRIS BUFFER, PH 7.8-8.2; 100 MM MGCL2; 1% OCTYL-BETA- D-GLUCOPYRANOSIDE
Resolution 2.00 Å
1A9S BOVINE PURINE NUCLEOSIDE PHOSPHORYLASE COMPLEXED WITH INOSINE AND SULFATE Deposited 1998-04-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–289（289 aa）
Not recorded SO4 SULFATE ION × 3 NOS INOSINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions PROTEIN WAS CRYSTALLIZED FROM 31-35% PEG-400 IN 100 MM HEPES BUFFER, PH 7.8-8.2; 100 MM MGCL2; 1% OCTYL-BETA- D-GLUCOPYRANOSIDE. CRYSTAL SOAKED IN 12.8 MM INOSINE AND 12 MM SULFATE.
Resolution 2.00 Å
1A9T BOVINE PURINE NUCLEOSIDE PHOSPHORYLASE COMPLEXED WITH 9-DEAZAINOSINE AND PHOSPHATE Deposited 1998-04-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–284（284 aa）
Not recorded R1P 1-O-phosphono-alpha-D-ribofuranose × 3 HPA HYPOXANTHINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions PROTEIN WAS CRYSTALLIZED FROM 31-35% PEG-400 IN 100 MM HEPES OR TRIS BUFFER, PH 7.8-8.2; 100 MM MGCL2; 1% OCTYL-BETA- D-GLUCOPYRANOSIDE
Resolution 2.00 Å
1B8N PURINE NUCLEOSIDE PHOSPHORYLASE Deposited 1999-02-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–284（284 aa）
Not recorded MG MAGNESIUM ION × 1 PO4 PHOSPHATE ION × 1 IMG 1,4-DIDEOXY-1,4-IMINO-1-(S)-(9-DEAZAGUANIN-9-YL)-D-RIBITOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；pH 8.0
Resolution 2.00 Å R-free 0.246
1B8N PURINE NUCLEOSIDE PHOSPHORYLASE Deposited 1999-02-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–284（284 aa）
Not recorded MG MAGNESIUM ION × 3 PO4 PHOSPHATE ION × 3 IMG 1,4-DIDEOXY-1,4-IMINO-1-(S)-(9-DEAZAGUANIN-9-YL)-D-RIBITOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；pH 8.0
Resolution 2.00 Å R-free 0.246
1B8O PURINE NUCLEOSIDE PHOSPHORYLASE Deposited 1999-02-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–284（284 aa）
Not recorded MG MAGNESIUM ION × 1 PO4 PHOSPHATE ION × 1 IMH 1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；PEG-400, TRIS, MGCL2, K3PO4, pH 8.0
Resolution 1.50 Å R-free 0.232
1B8O PURINE NUCLEOSIDE PHOSPHORYLASE Deposited 1999-02-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–284（284 aa）
Not recorded MG MAGNESIUM ION × 3 PO4 PHOSPHATE ION × 3 IMH 1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；PEG-400, TRIS, MGCL2, K3PO4, pH 8.0
Resolution 1.50 Å R-free 0.232
1FXU PURINE NUCLEOSIDE PHOSPHORYLASE FROM CALF SPLEEN IN COMPLEX WITH N(7)-ACYCLOGUANOSINE INHIBITOR AND A PHOSPHATE ION Deposited 2000-09-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–289（289 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 GU7 2-AMINO-7-[2-(2-HYDROXY-1-HYDROXYMETHYL-ETHYLAMINO)-ETHYL]-1,7-DIHYDRO-PURIN-6-ONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.04M Tris/HCl buffer, PEG 4000, 11-16%, 0.08M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Resolution 2.20 Å R-free 0.244
1FXU PURINE NUCLEOSIDE PHOSPHORYLASE FROM CALF SPLEEN IN COMPLEX WITH N(7)-ACYCLOGUANOSINE INHIBITOR AND A PHOSPHATE ION Deposited 2000-09-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–289（289 aa）
Not recorded MG MAGNESIUM ION × 3 ZN ZINC ION × 3 PO4 PHOSPHATE ION × 3 GU7 2-AMINO-7-[2-(2-HYDROXY-1-HYDROXYMETHYL-ETHYLAMINO)-ETHYL]-1,7-DIHYDRO-PURIN-6-ONE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.04M Tris/HCl buffer, PEG 4000, 11-16%, 0.08M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Resolution 2.20 Å R-free 0.244
1FXU PURINE NUCLEOSIDE PHOSPHORYLASE FROM CALF SPLEEN IN COMPLEX WITH N(7)-ACYCLOGUANOSINE INHIBITOR AND A PHOSPHATE ION Deposited 2000-09-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–289（289 aa）
Not recorded MG MAGNESIUM ION × 3 ZN ZINC ION × 3 PO4 PHOSPHATE ION × 3 GU7 2-AMINO-7-[2-(2-HYDROXY-1-HYDROXYMETHYL-ETHYLAMINO)-ETHYL]-1,7-DIHYDRO-PURIN-6-ONE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.04M Tris/HCl buffer, PEG 4000, 11-16%, 0.08M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Resolution 2.20 Å R-free 0.244
1LV8 Crystal structure of calf spleen purine nucleoside phosphorylase in a new space group with full trimer in the asymmetric unit Deposited 2002-05-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–289（289 aa）
Chain B 1–289（289 aa）
Chain C 1–289（289 aa）
Chain D 1–289（289 aa）
Chain E 1–289（289 aa）
Chain F 1–289（289 aa）
Not recorded CA CALCIUM ION × 6 9PP 2,6-DIAMINO-(S)-9-[2-(PHOSPHONOMETHOXY)PROPYL]PURINE × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.25；298 K；HEPES, PEG400, CaCl2, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.30 Å R-free 0.258
1LVU Crystal structure of calf spleen purine nucleoside phosphorylase in a new space group with full trimer in the asymmetric unit Deposited 2002-05-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–289（289 aa）
Chain B 1–289（289 aa）
Chain C 1–289（289 aa）
Chain D 1–289（289 aa）
Chain E 1–289（289 aa）
Chain F 1–289（289 aa）
Not recorded CA CALCIUM ION × 10 9PP 2,6-DIAMINO-(S)-9-[2-(PHOSPHONOMETHOXY)PROPYL]PURINE × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.25；286 K；PEG400, CaCl2, HEPES, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 286K
Resolution 2.05 Å R-free 0.244
1PBN PURINE NUCLEOSIDE PHOSPHORYLASE Deposited 1995-07-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–289（289 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å R-free 0.270
1V48 Calf spleen purine nucleoside phosphorylase (PNP) binary complex with 9-(5,5-difluoro-5-phosphonopenthyl)guanine Deposited 2003-11-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–289（289 aa）
Not recorded ZN ZINC ION × 3 MG MAGNESIUM ION × 3 HA1 9-(5,5-DIFLUORO-5-PHOSPHONOPENTYL)GUANINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.75；291 K；PEG 4000, Hepes, magnesium chloride, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.20 Å R-free 0.242
1V48 Calf spleen purine nucleoside phosphorylase (PNP) binary complex with 9-(5,5-difluoro-5-phosphonopenthyl)guanine Deposited 2003-11-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–289（289 aa）
Not recorded ZN ZINC ION × 3 MG MAGNESIUM ION × 3 HA1 9-(5,5-DIFLUORO-5-PHOSPHONOPENTYL)GUANINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.75；291 K；PEG 4000, Hepes, magnesium chloride, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.20 Å R-free 0.242
1VFN PURINE NUCLEOSIDE PHOSPHORYLASE Deposited 1996-10-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 4–284（281 aa）
Not recorded MG MAGNESIUM ION × 3 ZN ZINC ION × 3 HPA HYPOXANTHINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；16%(W/V) PEG 4000, 0.04M TRIS-HCL BUFFER PH 8.2-8.5, 0.08M MGCL2, pH 8.0
Resolution 2.15 Å
1VFN PURINE NUCLEOSIDE PHOSPHORYLASE Deposited 1996-10-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 4–284（281 aa）
Not recorded MG MAGNESIUM ION × 3 ZN ZINC ION × 3 HPA HYPOXANTHINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；16%(W/V) PEG 4000, 0.04M TRIS-HCL BUFFER PH 8.2-8.5, 0.08M MGCL2, pH 8.0
Resolution 2.15 Å
2AI1 Purine nucleoside phosphorylase from calf spleen Deposited 2005-07-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–289（289 aa）
Not recorded MG MAGNESIUM ION × 3 ZN ZINC ION × 3 144 TRIS-HYDROXYMETHYL-METHYL-AMMONIUM × 3 P1G ((2R,4R,6R,6AS)-4-(2-AMINO-6-OXO-1,6-DIHYDROPURIN-9-YL)-6-(HYDROXYMETHYL)-TETRAHYDROFURO[3,4-D][1,3]DIOXOL-2-YL)METHYLPHOSPHONIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；296 K；PEG2K MME, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 2.00 Å R-free 0.254
2AI1 Purine nucleoside phosphorylase from calf spleen Deposited 2005-07-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–289（289 aa）
Not recorded MG MAGNESIUM ION × 3 ZN ZINC ION × 3 144 TRIS-HYDROXYMETHYL-METHYL-AMMONIUM × 3 P1G ((2R,4R,6R,6AS)-4-(2-AMINO-6-OXO-1,6-DIHYDROPURIN-9-YL)-6-(HYDROXYMETHYL)-TETRAHYDROFURO[3,4-D][1,3]DIOXOL-2-YL)METHYLPHOSPHONIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；296 K；PEG2K MME, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 2.00 Å R-free 0.254
2AI2 Purine nucleoside phosphorylase from calf spleen Deposited 2005-07-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–289（289 aa）
Not recorded MG MAGNESIUM ION × 3 ZN ZINC ION × 3 144 TRIS-HYDROXYMETHYL-METHYL-AMMONIUM × 3 P1D ((2S,3AS,4R,6S)-4-(HYDROXYMETHYL)-6-(4-OXO-4,5-DIHYDRO-3H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)-TETRAHYDROFURO[3,4-D][1,3]DIOXO L-2-YL)METHYLPHOSPHONIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；296 K；PEG2K MME , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 1.70 Å R-free 0.231
2AI2 Purine nucleoside phosphorylase from calf spleen Deposited 2005-07-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–289（289 aa）
Not recorded MG MAGNESIUM ION × 3 ZN ZINC ION × 3 144 TRIS-HYDROXYMETHYL-METHYL-AMMONIUM × 3 P1D ((2S,3AS,4R,6S)-4-(HYDROXYMETHYL)-6-(4-OXO-4,5-DIHYDRO-3H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)-TETRAHYDROFURO[3,4-D][1,3]DIOXO L-2-YL)METHYLPHOSPHONIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；296 K；PEG2K MME , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 1.70 Å R-free 0.231
2AI3 Purine nucleoside phosphorylase from calf spleen Deposited 2005-07-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–289（289 aa）
Not recorded MG MAGNESIUM ION × 3 ZN ZINC ION × 3 144 TRIS-HYDROXYMETHYL-METHYL-AMMONIUM × 3 P2G (2S,4R,6R,6AS)-4-(2-AMINO-6-OXO-1,6-DIHYDROPURIN-9-YL)-6-(HYDROXYMETHYL)-TETRAHYDROFURO[3,4-D][1,3]DIOXOL-2-YLPHOSPHONI C ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；296 K；PEG2K MME , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 1.70 Å R-free 0.253
3FUC Recombinant calf purine nucleoside phosphorylase in a binary complex with multisubstrate analogue inhibitor 9-(5',5'-difluoro-5'-phosphonopentyl)-9-deazaguanine structure in a new space group with one full trimer in the asymmetric unit Deposited 2009-01-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–284（284 aa） Fragment：residues 1-284
Chain B 1–284（284 aa） Fragment：residues 1-284
Chain C 1–284（284 aa） Fragment：residues 1-284
Not recorded 9D9 [5-(2-amino-4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)-1,1-difluoropentyl]phosphonic acid × 3 MG MAGNESIUM ION × 3 AZI AZIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.7；298 K；33% PEG 400, 0.1M SODIUM AZIDE, 0.1M HEPES, 0.1M MAGNESIUM CHLORIDE, 1% OCTYL BETA-D-GLUCOPYRANOSIDE, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.45 Å R-free 0.199
3PNP THE HIGH RESOLUTION CRYSTAL STRUCTURE OF BOVINE SPLEEN PURINE NUCLEOSIDE PHOSPHORYLASE IN COMPLEX FORMS WITH PHOSPHATE AND 9-DEAZAINOSINE Deposited 1998-03-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–289（289 aa）
Not recorded MG MAGNESIUM ION × 3 PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；pH 8.0
Resolution 1.60 Å R-free 0.232
4PNP THE HIGH RESOLUTION CRYSTAL STRUCTURE OF BOVINE SPLEEN PURINE NUCLEOSIDE PHOSPHORYLASE IN COMPLEX FORMS WITH PHOSPHATE AND 9-DEAZAINOSINE Deposited 1998-03-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–289（289 aa）
Not recorded PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.1；pH 8.1
Resolution 1.80 Å R-free 0.248

20 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PNPH_BOVIN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–282； UniProt 3–284

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 2qpl

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2qpl
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2qpl
Deposition date deposition_date2007-07-24
Structure title titleCrystal structure of calf spleen purine nucleoside phosphorylase complexed to a novel purine analogue
Keywords keywordsPurine Nucleoside Phosphorylase, Acetylation, Glycosyltransferase, Transferase; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier19.09 Å
Radius of gyration Rg (electron density) rg_electron17.85 Å
Forward intensity I(0) i016242800.00
Molecular weight molecular_weight29860.0 kDa
Excluded volume excluded_volume37151 ų
Envelope volume envelope_volume42336 ų
Hydration-shell volume shell_volume19498 ų
Envelope diameter envelope_diameter61.1 Å
Shell Rg shell_rg24.45 Å
Envelope Rg envelope_rg18.14 Å
Shape Rg shape_rg17.86 Å
Total Rg total_rg18.76 Å
Total atoms total_atoms2097
Residues n_residues266
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax61.0 Å
Rg (real space) rg_real18.97 Å
Rg uncertainty (real space) rg_real_error0.26 Å
I(0) (real space) i0_real1.6240e+07
I(0) uncertainty (real space) i0_real_error1.7760e+05
Rg (reciprocal space) rg_reciprocal18.99 Å
I(0) (reciprocal space) i0_reciprocal16240000.0000
Solution quality estimate total_estimate0.8904
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.7 Å
Skewness Skewness skewness0.175
Kurtosis Kurtosis kurtosis-0.365
Angular range angular_range— – 0.4150 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha4104000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.860; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.996
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2qpla_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamilyc.56.2 — Purine and uridine phosphorylases
Family Family familyc.56.2.1 — Purine and uridine phosphorylases

CATH v4.4 (1 domains)

Domain ID domain_id2qplA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1580 — Nucleoside phosphorylase domain
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8. Citations (1)

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9. Files and Curves (10)