2C11

Crystal structure of the 2-hydrazinopyridine of semicarbazide- sensitive amine oxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 

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Ligand Structure Quality Assessment 


This is version 3.0 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: 10.1107/S0907444905028805
  • Primary Citation of Related Structures:  
    2C11, 2C10

  • 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MEMBRANE COPPER AMINE OXIDASEA, B, C, D735Homo sapiensMutation(s): 0 
Gene Names: AOC3VAP1
EC: 1.4.3.6 (PDB Primary Data), 1.4.3.21 (UniProt)
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q16853 (Homo sapiens)
Explore Q16853 
Go to UniProtKB:  Q16853
PHAROS:  Q16853
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE, I2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseF2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG, K3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D 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-glucopyranoseH, L5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42466VF
GlyCosmos:  G42466VF
GlyGen:  G42466VF
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseJ3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth B] , AB [auth D] , BA [auth B] , BB [auth D] , M [auth A] , MA [auth C] , N [auth A] , NA [auth C] , 
AA [auth B],  AB [auth D],  BA [auth B],  BB [auth D],  M [auth A],  MA [auth C],  N [auth A],  NA [auth C],  Z [auth B],  ZA [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CU
Query on CU

Download Ideal Coordinates CCD File 
DA [auth B] , DB [auth D] , FA [auth B] , GA [auth B] , GB [auth D] , HA [auth B] , HB [auth D] , IA [auth B] , 
DA [auth B],  DB [auth D],  FA [auth B],  GA [auth B],  GB [auth D],  HA [auth B],  HB [auth D],  IA [auth B],  IB [auth D],  JA [auth B],  JB [auth D],  KA [auth B],  KB [auth D],  LA [auth B],  LB [auth D],  P [auth A],  PA [auth C],  S [auth A],  SA [auth C],  T [auth A],  TA [auth C],  U [auth A],  UA [auth C],  V [auth A],  VA [auth C],  W [auth A],  WA [auth C],  X [auth A],  XA [auth C],  YA [auth C]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
CA [auth B], CB [auth D], EA [auth B], EB [auth D], O [auth A], OA [auth C], Q [auth A], QA [auth C]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
FB [auth D], R [auth A], RA [auth C], Y [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PAQ
Query on PAQ
A, B, C, DL-PEPTIDE LINKINGC14 H16 N4 O4TYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.402α = 90
b = 127.402β = 90
c = 219.361γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

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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: 2011-08-03
    Changes: Atomic model, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 2.0: 2018-10-17
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Refinement 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