4DY0

Crystal structure of native protease nexin-1 with heparin

• PDB DOI: https://doi.org/10.2210/pdb4DY0/pdb

• Classification: HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-02-28 Released: 2012-08-15 
• Deposition Author(s): Huntington, J.A., Li, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.226 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 84.99 kDa 
• Atom Count: 5,947 
• Modelled Residue Count: 732 
• Deposited Residue Count: 758 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glia-derived nexin	A, B	379	Homo sapiens	Mutation(s): 0  Gene Names: SERPINE2, PI7, PN1
UniProt & NIH Common Fund Data Resources
Find proteins for P07093 (Homo sapiens) Explore P07093  Go to UniProtKB:  P07093
PHAROS:  P07093 GTEx:  ENSG00000135919

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid	C	2		N/A
Glycosylation Resources
GlyTouCan:  G29057GU GlyCosmos:  G29057GU GlyGen:  G29057GU

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], F [auth B], G [auth B], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.226 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.65	α = 90
b = 140.65	β = 90
c = 93.55	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-15 
Deposition Author(s): Huntington, J.A., Li, W.

Revision History  

• Version 1.0: 2012-08-15
  Type: Initial release
  
• Version 1.1: 2015-04-22
  Changes: Non-polymer description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Source and taxonomy, Structure summary
• Version 2.1: 2024-02-28
  Changes: Data collection, Database references, Structure summary
• Version 2.2: 2024-03-13
  Changes: Source and taxonomy, Structure summary