1nd5

Crystal Structures of Human Prostatic Acid Phosphatase in Complex with a Phosphate Ion and alpha-Benzylaminobenzylphosphonic Acid Update the Mechanistic Picture and Offer New Insights into Inhibitor Design

Method: X-RAY DIFFRACTION Dmax: 130.8 Å Quality: GOOD

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

prostatic acid phosphatase

OrganismNot specified

UniProt P15309

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Homooligomer Protein × 3 其他Polymer 4 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 33–386 Chain B; UniProt 33–386 Chain C; UniProt 33–386 Not recorded 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 2BF ALPHA-BENZYL-AMINOBENZYL-PHOSPHONIC ACID × 3 1PE PENTAETHYLENE GLYCOL × 7 NDG 2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 10;298 K;PEG, KCL, Glycine, pH 10.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.90 Å R-free 0.279
2 Other combination Homooligomer Protein × 2 其他Polymer 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 33–386 Chain D; UniProt 33–386 Not recorded 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2BF ALPHA-BENZYL-AMINOBENZYL-PHOSPHONIC ACID × 2 1PE PENTAETHYLENE GLYCOL × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 10;298 K;PEG, KCL, Glycine, pH 10.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.90 Å R-free 0.279

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.

16 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PPAP_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–354; UniProt 33–386 Author chain B; PDBConstruct 1–354; UniProt 33–386 Author chain C; PDBConstruct 1–354; UniProt 33–386 Author chain D; PDBConstruct 1–354; UniProt 33–386

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 1nd5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1nd5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1nd5
Deposition date deposition_date2002-12-07
Structure title titleCrystal Structures of Human Prostatic Acid Phosphatase in Complex with a Phosphate Ion and alpha-Benzylaminobenzylphosphonic Acid Update the Mechanistic Picture and Offer New Insights into Inhibitor Design
Keywords keywordsAcid Phosphatase, PAP, Prostate, Phosphate, inhibitor, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier37.63
Radius of gyration Rg (electron density) rg_electron37.32
Forward intensity I(0) i0386764000.00
Molecular weight molecular_weight164630.0 kDa
Excluded volume excluded_volume207750 ų
Envelope volume envelope_volume255780 ų
Hydration-shell volume shell_volume57408 ų
Envelope diameter envelope_diameter142.3
Shell Rg shell_rg43.13
Envelope Rg envelope_rg37.11
Shape Rg shape_rg37.31
Total Rg total_rg37.70
Total atoms total_atoms11592
Residues n_residues1368
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 dmax130.8
Rg (real space) rg_real37.68
Rg uncertainty (real space) rg_real_error0.84
I(0) (real space) i0_real3.8680e+08
I(0) uncertainty (real space) i0_real_error5.0540e+06
Rg (reciprocal space) rg_reciprocal37.65
I(0) (reciprocal space) i0_reciprocal386800000.0000
Solution quality estimate total_estimate0.8699
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary43.6
Skewness Skewness skewness0.426
Kurtosis Kurtosis kurtosis-0.151
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0005
Highest regularization parameter α highest_alpha116100000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.783; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.956

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1nd5a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.60 — Phosphoglycerate mutase-like
Superfamily Superfamily superfamilyc.60.1 — Phosphoglycerate mutase-like
Family Family familyc.60.1.2 — Histidine acid phosphatase
Domain ID domain_idd1nd5b_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.60 — Phosphoglycerate mutase-like
Superfamily Superfamily superfamilyc.60.1 — Phosphoglycerate mutase-like
Family Family familyc.60.1.2 — Histidine acid phosphatase
Domain ID domain_idd1nd5c_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.60 — Phosphoglycerate mutase-like
Superfamily Superfamily superfamilyc.60.1 — Phosphoglycerate mutase-like
Family Family familyc.60.1.2 — Histidine acid phosphatase
Domain ID domain_idd1nd5d_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.60 — Phosphoglycerate mutase-like
Superfamily Superfamily superfamilyc.60.1 — Phosphoglycerate mutase-like
Family Family familyc.60.1.2 — Histidine acid phosphatase

CATH v4.4 (4 domains)

Domain ID domain_id1nd5A00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1240 — Phosphoglycerate mutase-like
Domain ID domain_id1nd5B00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1240 — Phosphoglycerate mutase-like
Domain ID domain_id1nd5C00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1240 — Phosphoglycerate mutase-like
Domain ID domain_id1nd5D00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1240 — Phosphoglycerate mutase-like

8. Citations (1)

9. Files and Curves (10)