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1d6a

STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN COMPLEXED WITH GUANINE

Method: X-RAY DIFFRACTION Dmax: 129.6 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

POKEWEED ANTIVIRAL PROTEIN

OrganismNot specified

UniProt P10297

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 23–284 Not recorded GUN GUANINE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；16-18% PEG 4000, 0.1M CACL2, 5MM GUANINE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.10 Å R-free 0.250
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 23–284 Not recorded GUN GUANINE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；16-18% PEG 4000, 0.1M CACL2, 5MM GUANINE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.10 Å R-free 0.250

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 1D6A Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1PAF THE 2.5 ANGSTROMS STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN Deposited 1992-10-19 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–284（262 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
1PAF THE 2.5 ANGSTROMS STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN Deposited 1992-10-19 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 23–284（262 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
1PAG THE 2.5 ANGSTROMS STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN Deposited 1992-10-19 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–284（262 aa）
Not recorded FMP FORMYCIN-5'-MONOPHOSPHATE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å
1PAG THE 2.5 ANGSTROMS STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN Deposited 1992-10-19 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 23–284（262 aa）
Not recorded FMP FORMYCIN-5'-MONOPHOSPHATE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å
1QCG LOW TEMPERATURE STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN Deposited 1999-05-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–263（262 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290 K；16-18% PEG 4000, 0.1M CACL2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.10 Å R-free 0.270
1QCG LOW TEMPERATURE STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN Deposited 1999-05-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–263（262 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290 K；16-18% PEG 4000, 0.1M CACL2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.10 Å R-free 0.270
1QCI LOW TEMPERATURE STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN COMPLEXED WITH ADENINE Deposited 1999-05-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–263（262 aa）
Not recorded ADE ADENINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290 K；16-18% PEG 4000, 0.1M CACL2, 5MM ADENYL(3'-5')GUANOSINE, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.00 Å
1QCI LOW TEMPERATURE STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN COMPLEXED WITH ADENINE Deposited 1999-05-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–263（262 aa）
Not recorded ADE ADENINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290 K；16-18% PEG 4000, 0.1M CACL2, 5MM ADENYL(3'-5')GUANOSINE, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.00 Å
1QCJ LOW TEMPERATURE COMPLEX OF POKEWEED ANTIVIRAL PROTEIN WITH PTEORIC ACID Deposited 1999-05-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–263（262 aa）
Not recorded APT 2-AMINO-6-[(4-CARBOXY-PHENYLAMINO)-METHYL]-4-HYDROXY-PTERIDIN-1-IUM × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290 K；16-18% PEG 4000, 0.1M CACL2, PTEORIC ACID, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.10 Å R-free 0.230
1QCJ LOW TEMPERATURE COMPLEX OF POKEWEED ANTIVIRAL PROTEIN WITH PTEORIC ACID Deposited 1999-05-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–263（262 aa）
Not recorded APT 2-AMINO-6-[(4-CARBOXY-PHENYLAMINO)-METHYL]-4-HYDROXY-PTERIDIN-1-IUM × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290 K；16-18% PEG 4000, 0.1M CACL2, PTEORIC ACID, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.10 Å R-free 0.230

5 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RIP1_PHYAM
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–262； UniProt 23–284 Author chain B； PDBConstruct 1–262； UniProt 23–284

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 1d6a

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1d6a
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1d6a
Deposition date deposition_date1999-10-12
Structure title titleSTRUCTURE OF POKEWEED ANTIVIRAL PROTEIN COMPLEXED WITH GUANINE
Keywords keywordsPOKEWEED ANTIVIRAL PROTEIN, RIBOSOME INACTIVATING PROTEIN, HYDROLASE; HYDROLASE
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_guinier41.80 Å
Radius of gyration Rg (electron density) rg_electron41.64 Å
Forward intensity I(0) i052031600.00
Molecular weight molecular_weight58932.0 kDa
Excluded volume excluded_volume73904 ų
Envelope volume envelope_volume107730 ų
Hydration-shell volume shell_volume21652 ų
Envelope diameter envelope_diameter129.0 Å
Shell Rg shell_rg47.82 Å
Envelope Rg envelope_rg38.98 Å
Shape Rg shape_rg41.62 Å
Total Rg total_rg42.02 Å
Total atoms total_atoms5128
Residues n_residues524
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 dmax129.6 Å
Rg (real space) rg_real42.14 Å
Rg uncertainty (real space) rg_real_error1.47 Å
I(0) (real space) i0_real5.2030e+07
I(0) uncertainty (real space) i0_real_error8.5910e+05
Rg (reciprocal space) rg_reciprocal41.81 Å
I(0) (reciprocal space) i0_reciprocal52010000.0000
Solution quality estimate total_estimate0.5989
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.9 Å
Skewness Skewness skewness0.162
Kurtosis Kurtosis kurtosis-1.369
Angular range angular_range— – 0.1900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6095000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.010; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.130; Smooth: 0.622
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1d6aa_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.165 — Ribosome inactivating proteins (RIP)
Superfamily Superfamily superfamilyd.165.1 — Ribosome inactivating proteins (RIP)
Family Family familyd.165.1.1 — Plant cytotoxins
Domain ID domain_idd1d6ab_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.165 — Ribosome inactivating proteins (RIP)
Superfamily Superfamily superfamilyd.165.1 — Ribosome inactivating proteins (RIP)
Family Family familyd.165.1.1 — Plant cytotoxins

CATH v4.4 (4 domains)

Domain ID domain_id1d6aA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology420 — Ricin (A subunit); domain 1
Homologous superfamily homologous superfamily10 — Ricin (A subunit), domain 1
Domain ID domain_id1d6aA02
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology470 — Ricin (A Subunit), domain 2
Homologous superfamily homologous superfamily10 — Ricin (A Subunit), domain 2
Domain ID domain_id1d6aB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology420 — Ricin (A subunit); domain 1
Homologous superfamily homologous superfamily10 — Ricin (A subunit), domain 1
Domain ID domain_id1d6aB02
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology470 — Ricin (A Subunit), domain 2
Homologous superfamily homologous superfamily10 — Ricin (A Subunit), domain 2
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8. Citations (1)

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9. Files and Curves (10)