3D0G

Crystal structure of spike protein receptor-binding domain from the 2002-2003 SARS coronavirus human strain complexed with human-civet chimeric receptor ACE2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history



Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Angiotensin-converting enzyme 2
A, B
597Paguma larvataHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: ACE2UNQ868/PRO1885
EC: 3.4.17.23
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens)
Explore Q9BYF1 
Go to UniProtKB:  Q9BYF1
PHAROS:  Q9BYF1
GTEx:  ENSG00000130234 
Find proteins for Q56NL1 (Paguma larvata)
Explore Q56NL1 
Go to UniProtKB:  Q56NL1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9BYF1Q56NL1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoproteinC [auth E],
D [auth F]
179Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: S2
UniProt
Find proteins for P59594 (Severe acute respiratory syndrome coronavirus)
Explore P59594 
Go to UniProtKB:  P59594
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59594
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
M [auth E]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
NDG
Query on NDG

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E [auth A],
H [auth B],
I [auth B],
J [auth B],
N [auth F]
2-acetamido-2-deoxy-alpha-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.008α = 90
b = 119.762β = 96.22
c = 108.801γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2008-07-08 
  • Deposition Author(s): Li, F.

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-06-21
    Changes: Refinement description, Source and taxonomy, Structure summary
  • Version 1.3: 2017-10-25
    Changes: Refinement description
  • Version 1.4: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary