5E8M
Crystal structure of human heparanase
- PDB DOI: https://doi.org/10.2210/pdb5E8M/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Trichoplusia ni
- Mutation(s): Yes 
- Deposited: 2015-10-14 Released: 2015-11-18 
- Funding Organization(s): European Research Council
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.75 Å
- R-Value Free: 0.200 
- R-Value Work: 0.164 
- R-Value Observed: 0.166 
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 |
Heparanase | 389 | Homo sapiens | Mutation(s): 1  Gene Names: HPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1 EC: 3.2.1.166 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9Y251 (Homo sapiens) Explore Q9Y251  Go to UniProtKB:  Q9Y251 | |||||
PHAROS:  Q9Y251 GTEx:  ENSG00000173083  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9Y251 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Heparanase | 77 | Homo sapiens | Mutation(s): 0  Gene Names: HPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1 EC: 3.2.1.166 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9Y251 (Homo sapiens) Explore Q9Y251  Go to UniProtKB:  Q9Y251 | |||||
PHAROS:  Q9Y251 GTEx:  ENSG00000173083  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9Y251 | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | D [auth A], E [auth A], F [auth A], G [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
EDO Query on EDO | H [auth A] I [auth A] J [auth A] K [auth A] L [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N | |||
CL Query on CL | V [auth A], W [auth A], X [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.75 Å
- R-Value Free: 0.200 
- R-Value Work: 0.164 
- R-Value Observed: 0.166 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 46.765 | α = 90 |
b = 70.972 | β = 94.17 |
c = 78.948 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
SHELX | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2015-11-18  Deposition Author(s): Wu, L., Davies, G.J.
Funding Organization | Location | Grant Number |
---|---|---|
European Research Council | United Kingdom | -- |
Revision History (Full details and data files)
- Version 1.0: 2015-11-18
Type: Initial release - Version 1.1: 2015-12-02
Changes: Database references - Version 1.2: 2015-12-16
Changes: Database references - Version 1.3: 2016-05-04
Changes: Structure summary - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary