5E97

Glycoside Hydrolase ligand structure 1

• PDB DOI: https://doi.org/10.2210/pdb5E97/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2015-10-14 Released: 2015-11-18 
• Deposition Author(s): Wu, L., Davies, G.J.
• Funding Organization(s): European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.197 
• R-Value Work: 0.166 
• R-Value Observed: 0.167 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 54.22 kDa 
• Atom Count: 4,171 
• Modelled Residue Count: 459 
• Deposited Residue Count: 466 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heparanase	A	389	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heparanase	B	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

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid	C	4		N/A
Glycosylation Resources
GlyTouCan:  G35277LL GlyCosmos:  G35277LL GlyGen:  G35277LL

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
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
NPO	K [auth A]	P-NITROPHENOL C6 H5 N O3 BTJIUGUIPKRLHP-UHFFFAOYSA-N
CL	H [auth A], I [auth A], J [auth A], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.197 
• R-Value Work: 0.166 
• R-Value Observed: 0.167 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.88	α = 90
b = 70.89	β = 94.91
c = 78.23	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-11-18 
Deposition Author(s): Wu, L., Davies, G.J.

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Funding Organization	Location	Grant Number
European Research Council	United Kingdom	--

Revision History  

• 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 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary