4DY0

Crystal structure of native protease nexin-1 with heparin

Structural Biology Knowledgebase: 4DY0 SBKB.org


Experimental Data Snapshot

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

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DY0

Classification: HYDROLASE INHIBITOR

Total Structure Weight: 84995.69

Macromolecule Entities
Molecule Chains Length Organism Details
Glia-derived nexin A, B 379 Homo sapiens Gene Name(s): SERPINE2 Gene View PI7 PN1

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SGN
Query on SGN

A N,O6-DISULFO-GLUCOSAMINE
C6 H13 N O11 S2
DQTRACMFIGDHSN-UKFBFLRUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IDS
Query on IDS

A 2-O-sulfo-alpha-L-idopyranuronic acid
O2-SULFO-GLUCURONIC ACID (Synonym)
C6 H10 O10 S
COJBCAMFZDFGFK-VCSGLWQLSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.182
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 140.65 α = 90.00
b = 140.65 β = 90.00
c = 93.55 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

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

Revision History

  • 2015-04-22
    Type: Non-polymer description | Details: Correct entity category