3KM9

Structure of complement C5 in complex with the C-terminal beta-grasp domain of SSL7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history



Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C5A,
C [auth B]
1,676Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01031 (Homo sapiens)
Explore P01031 
Go to UniProtKB:  P01031
PHAROS:  P01031
GTEx:  ENSG00000106804 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01031
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Staphylococcal enterotoxin-like toxinB [auth X],
D [auth Y]
103Staphylococcus aureus subsp. aureus str. NewmanMutation(s): 0 
UniProt
Find proteins for A0A0H3K6Z8 (Staphylococcus aureus (strain Newman))
Explore A0A0H3K6Z8 
Go to UniProtKB:  A0A0H3K6Z8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3K6Z8
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth C],
F [auth D]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.79α = 90
b = 144.79β = 90
c = 245.28γ = 120
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary