1BNL

ZINC DEPENDENT DIMERS OBSERVED IN CRYSTALS OF HUMAN ENDOSTATIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Zinc-dependent dimers observed in crystals of human endostatin.

Ding, Y.H.Javaherian, K.Lo, K.M.Chopra, R.Boehm, T.Lanciotti, J.Harris, B.A.Li, Y.Shapiro, R.Hohenester, E.Timpl, R.Folkman, J.Wiley, D.C.

(1998) Proc.Natl.Acad.Sci.USA 95: 10443-10448


  • PubMed Abstract: 
  • The crystal structure of human endostatin reveals a zinc-binding site. Atomic absorption spectroscopy indicates that zinc is a constituent of both human and murine endostatin in solution. The human endostatin zinc site is formed by three histidines a ...

    The crystal structure of human endostatin reveals a zinc-binding site. Atomic absorption spectroscopy indicates that zinc is a constituent of both human and murine endostatin in solution. The human endostatin zinc site is formed by three histidines at the N terminus, residues 1, 3, and, 11, and an aspartic acid at residue 76. The N-terminal loop ordered around the zinc makes a dimeric contact in human endostatin crystals. The location of the zinc site at the amino terminus, immediately adjacent to the precursor cleavage site, suggests the possibility that the zinc may be involved in activation of the antiangiogenic activity following cleavage from the inactive collagen XVIII precursor or in the cleavage process itself.


    Organizational Affiliation

    Department of Cellular and Molecular Biology, Howard Hughes Medical Institute, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COLLAGEN XVIII
A, B, C, D
178Homo sapiensGene Names: COL18A1
Find proteins for P39060 (Homo sapiens)
Go to Gene View: COL18A1
Go to UniProtKB:  P39060
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.240 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 92.713α = 90.00
b = 74.266β = 102.55
c = 137.805γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
SCALEPACKdata scaling
DENZOdata reduction
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-10-14
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance