1US1

Crystal structure of human vascular adhesion protein-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.242 

wwPDB Validation 3D Report Full Report



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

  • DOI: 10.1110/ps.051438105
  • Primary Citation of Related Structures:  
    1PU4, 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.
      (2003) Acta Crystallogr D Biol Crystallogr 59: 1288

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MEMBRANE COPPER AMINE OXIDASEAB763Homo sapiensMutation(s): 0 
Gene Names: AOC3VAP1
EC: 1.4.3.6 (PDB Primary Data), 1.4.3.21 (UniProt)
Find proteins for Q16853 (Homo sapiens)
Explore Q16853 
Go to UniProtKB:  Q16853
NIH Common Fund Data Resources
PHAROS  Q16853
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
2 N-Glycosylation
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CU
Query on CU

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

Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPQ
Query on TPQ
A,BL-PEPTIDE LINKINGC9 H9 N O5TYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.242 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 226.099α = 90
b = 226.099β = 90
c = 223.004γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-02-16
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-02-28
    Changes: Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary