2WIN

C3 convertase (C3bBb) stabilized by SCIN

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.253 

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 C3 BETA CHAIN
A, C, E, G
645Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens)
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Go to UniProtKB:  P01024
PHAROS:  P01024
GTEx:  ENSG00000125730 
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UniProt GroupP01024
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
COMPLEMENT C3B ALPHA' CHAIN
B, D, F, H
915Homo sapiensMutation(s): 0 
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Go to UniProtKB:  P01024
PHAROS:  P01024
GTEx:  ENSG00000125730 
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UniProt GroupP01024
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
COMPLEMENT FACTOR B
I, J, K, L
507Homo sapiensMutation(s): 0 
EC: 3.4.21.47
UniProt & NIH Common Fund Data Resources
Find proteins for P00751 (Homo sapiens)
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PHAROS:  P00751
GTEx:  ENSG00000243649 
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UniProt GroupP00751
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
STAPHYLOCOCCAL COMPLEMENT INHIBITORM,
N,
O [auth P],
P [auth Q]		92Staphylococcus aureusMutation(s): 0 
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UniProt GroupQ6GFB4
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Oligosaccharides

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Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseQ [auth O],
R,
T,
U		4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G40894EI
GlyCosmos:  G40894EI
GlyGen:  G40894EI
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-3)-beta-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
S, W
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G82690UI
GlyCosmos:  G82690UI
GlyGen:  G82690UI
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-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
V
6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G36782MK
GlyCosmos:  G36782MK
GlyGen:  G36782MK
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
X
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G04854NQ
GlyCosmos:  G04854NQ
GlyGen:  G04854NQ
Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseAA [auth a],
Y		3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G62182OO
GlyCosmos:  G62182OO
GlyGen:  G62182OO
Entity ID: 10
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Z
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 11
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseBA [auth b]5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21381MC
GlyCosmos:  G21381MC
GlyGen:  G21381MC
Entity ID: 12
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseCA [auth c]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
JA [auth K],
LA [auth L]		2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN
Query on MAN
Download Ideal Coordinates CCD File 
EA [auth G]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
BMA
Query on BMA
Download Ideal Coordinates CCD File 
DA [auth B],
IA [auth K]		beta-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
FA [auth I],
GA [auth J],
HA [auth K],
KA [auth L]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.253 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 228.632α = 90
b = 121.491β = 91.64
c = 280.783γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-09
    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: 2018-01-17
    Changes: Advisory, Database references, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-12-13
    Changes: Advisory, Data collection, Database references, Refinement description, Structure summary