2C10 | pdb_00002c10

The structure of a truncated, soluble version of semicarbazide- sensitive amine oxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.252 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 3.1 of the entry. See complete history

Literature

Structure of human semicarbazide-sensitive amine oxidase/vascular adhesion protein-1.

Jakobsson, E.Nilsson, J.Ogg, D.Kleywegt, G.J.

(2005) Acta Crystallogr D Biol Crystallogr 61: 1550-1562

  • DOI: https://doi.org/10.1107/S0907444905028805
  • Primary Citation Related Structures: 
    2C10, 2C11

  • PubMed Abstract: 

    Semicarbazide-sensitive amine oxidase (SSAO) belongs to a ubiquitous family of copper-containing amine oxidases (CuAOs). SSAO is also known as vascular adhesion protein-1 (VAP-1) and has been identified as one of the adhesion molecules involved in the leukocyte-extravasation process. The structure of a truncated soluble form of human SSAO has been solved and refined to 2.5 A. As expected, SSAO is a homodimer with a fold typical of the CuAO family. The topaquinone (TPQ) cofactor and a copper ion characteristic of CuAOs are present in the active site, with the TPQ in the active ;off-copper' conformation. The structure reveals that a leucine residue (Leu469) located adjacent to the active site could function as a gate controlling its accessibility. An RGD motif is displayed on the surface, where it could be involved in integrin binding and possibly play a role in the shedding of SSAO from the membrane. Carbohydrate moieties are observed at five of six potential N-glycosylation sites. Carbohydrates attached to Asn232 flank the active-site entrance and might influence substrate specificity. The structure of an adduct of SSAO and the irreversible inhibitor 2-hydrazinopyridine has been solved and refined to 2.9 A resolution. Together, these structures will aid efforts to identify natural substrates, provide valuable information for the design of specific inhibitors and direct further studies.


  • Organizational Affiliation
    • Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, Sweden.

Macromolecule Content 

  • Total Structure Weight: 336.5 kDa 
  • Atom Count: 23,470 
  • Modeled Residue Count: 2,830 
  • Deposited Residue Count: 2,940 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MEMBRANE COPPER AMINE OXIDASE
A, B, C, D
735Homo sapiensMutation(s): 0 
EC: 1.4.3.6 (PDB Primary Data), 1.4.3.21 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q16853 (Homo sapiens)
Explore Q16853 
Go to UniProtKB:  Q16853
PHAROS:  Q16853
GTEx:  ENSG00000131471 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16853
Glycosylation
Glycosylation Sites: 5Go to GlyGen: Q16853-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, H, K
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
F, L
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB
GlyCosmos: G21290RB
GlyGen: G21290RB
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, J, M, P
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
I, O
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G42466VF
GlyCosmos: G42466VF
GlyGen: G42466VF
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
N
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G22573RC
GlyCosmos: G22573RC
GlyGen: G22573RC

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
EA [auth C]
KA [auth D]
LA [auth D]
MA [auth D]
Q [auth A]
EA [auth C],
KA [auth D],
LA [auth D],
MA [auth D],
Q [auth A],
W [auth B],
X [auth B],
Y [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CU

Query on CU



Download:Ideal Coordinates CCD File
AA [auth B],
GA [auth C],
OA [auth D],
S [auth A]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
BA [auth B]
FA [auth C]
HA [auth C]
NA [auth D]
PA [auth D]
BA [auth B],
FA [auth C],
HA [auth C],
NA [auth D],
PA [auth D],
R [auth A],
T [auth A],
Z [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
CA [auth B]
DA [auth B]
IA [auth C]
JA [auth C]
QA [auth D]
CA [auth B],
DA [auth B],
IA [auth C],
JA [auth C],
QA [auth D],
RA [auth D],
U [auth A],
V [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPQ
Query on TPQ
A, B, C, D
L-PEPTIDE LINKINGC9 H9 N O5TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.252 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.236α = 90
b = 130.236β = 90
c = 221.529γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 2.0: 2018-10-17
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation, Structure summary
  • Version 2.2: 2019-10-09
    Changes: Author supporting evidence, Data collection, Other, Structure summary
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.1: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary