1PU4

Crystal structure of human vascular adhesion protein-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the human vascular adhesion protein-1: unique structural features with functional implications.

Airenne, T.T.Nymalm, Y.Kidron, H.Smith, D.J.Pihlavisto, M.Salmi, M.Jalkanen, S.Johnson, M.S.Salminen, T.A.

(2005) Protein Sci. 14: 1964-1974

  • DOI: 10.1110/ps.051438105
  • Primary Citation of Related Structures:  1US1

  • PubMed Abstract: 
  • The expression of human vascular adhesion protein-1 (hVAP-1) is induced at sites of inflammation where extravasation of lymphocytes from blood to the peripheral tissue occurs. We have solved the X-ray structure of hVAP-1, a human copper amine oxidase ...

    The expression of human vascular adhesion protein-1 (hVAP-1) is induced at sites of inflammation where extravasation of lymphocytes from blood to the peripheral tissue occurs. We have solved the X-ray structure of hVAP-1, a human copper amine oxidase (CAO), which is distinguished from other CAOs in being membrane-bound. The dimer structure reveals some intriguing features that may have fundamental roles in the adhesive and enzymatic functions of hVAP-1, especially regarding the role of hVAP-1 in inflammation, lymphocyte attachment, and signaling. Firstly, Leu469 at the substrate channel may play a key role in controlling the substrate entry; depending on its conformation, it either blocks or gives access to the active site. Secondly, sugar units are clearly observed at two of the six predicted N-glycosylation sites. Moreover, mutagenesis analysis showed that all of the predicted sites were glycosylated in the protein used for crystallization. Thirdly, the existence of a solvent-exposed RGD motif at the entrance to each active site in hVAP-1 suggests that it may have a functional role.


    Related Citations: 
    • Crystallization and preliminary X-ray analysis of the human vascular adhesion protein-1
      Nymalm, Y.,Kidron, H.,Soderholm, A.,Viitanen, L.,Kaukonen, K.,Pihlavisto, M.,Smith, D.,Veromaa, T.,Airenne, T.T.,Johnson, M.S.,Salminen, T.A.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Department of Biochemistry and Pharmacy, Abo Akademi University, FIN-20520 Turku, Finland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Membrane copper amine oxidase
A, B
763Homo sapiensGene Names: AOC3 (VAP1)
EC: 1.4.3.21
Find proteins for Q16853 (Homo sapiens)
Go to Gene View: AOC3
Go to UniProtKB:  Q16853
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A, B
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPQ
Query on TPQ
A, B
L-PEPTIDE LINKINGC9 H9 N O5TYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.217 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 225.916α = 90.00
b = 225.916β = 90.00
c = 218.668γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-03
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance