3L5N

Staphylococcal Complement Inhibitor (SCIN) in complex with Human Complement Component C3b

• PDB DOI: https://doi.org/10.2210/pdb3L5N/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Staphylococcus aureus subsp. aureus Mu50
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-12-22 Released: 2010-08-04 
• Deposition Author(s): Geisbrecht, B.V., Garcia, B.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 7.54 Å
• R-Value Free: 0.268 
• R-Value Work: 0.265 
• R-Value Observed: 0.265 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 186.37 kDa 
• Atom Count: 12,785 
• Modelled Residue Count: 1,609 
• Deposited Residue Count: 1,648 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C3	A	645	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens) Explore P01024  Go to UniProtKB:  P01024
PHAROS:  P01024 GTEx:  ENSG00000125730

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C3	B	915	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens) Explore P01024  Go to UniProtKB:  P01024
PHAROS:  P01024 GTEx:  ENSG00000125730

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Staphylococcal complement inhibitor	C [auth M]	88	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0  Gene Names: SAV1942, scn
UniProt
Find proteins for Q931M7 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore Q931M7  Go to UniProtKB:  Q931M7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN	F [auth A]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 7.54 Å
• R-Value Free: 0.268 
• R-Value Work: 0.265 
• R-Value Observed: 0.265 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.026	α = 90
b = 128.026	β = 90
c = 468.591	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-04 
Deposition Author(s): Geisbrecht, B.V., Garcia, B.L.

Revision History  

• Version 1.0: 2010-08-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Advisory, Refinement description
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2023-09-06
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary