1ND6
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
- PDB DOI: https://doi.org/10.2210/pdb1ND6/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Mutation(s): No 
- Deposited: 2002-12-07 Released: 2002-12-20 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.256 
- R-Value Work: 0.198 
- R-Value Observed: 0.198 
wwPDB Validation   3D Report Full Report
This is version 2.0 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
prostatic acid phosphatase | 354 | Homo sapiens | Mutation(s): 0  EC: 3.1.3.2 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P15309 (Homo sapiens) Explore P15309  Go to UniProtKB:  P15309 | |||||
PHAROS:  P15309 GTEx:  ENSG00000014257  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P15309 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | E | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G04854NQ GlyCosmos:  G04854NQ GlyGen:  G04854NQ |
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | F | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | G | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G21381MC GlyCosmos:  G21381MC GlyGen:  G21381MC |
Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | H | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G62182OO GlyCosmos:  G62182OO GlyGen:  G62182OO |
Entity ID: 6 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | I | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G27747YT GlyCosmos:  G27747YT GlyGen:  G27747YT |
Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
1PE Query on 1PE | K [auth A], O [auth B], Q [auth C], T [auth D] | PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N | |||
NAG Query on NAG | L [auth B], R [auth D] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
PO4 Query on PO4 | J [auth A], M [auth B], P [auth C], S [auth D] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K | |||
GLY Query on GLY | N [auth B] | GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.256 
- R-Value Work: 0.198 
- R-Value Observed: 0.198 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 119.89 | α = 90 |
b = 203.32 | β = 90 |
c = 70.89 | γ = 90 |
Software Name | Purpose |
---|---|
HKL-2000 | data collection |
SCALEPACK | data scaling |
CNS | refinement |
HKL-2000 | data reduction |
CNS | phasing |
Entry History 
Deposition Data
- Released Date: 2002-12-20  Deposition Author(s): Ortlund, E., LaCount, M.W., Lebioda, L.
Revision History (Full details and data files)
- Version 1.0: 2002-12-20
Type: Initial release - Version 1.1: 2008-04-28
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary