5UBM

Crystal structure of human C1s in complex with inhibitor gigastasin

• PDB DOI: https://doi.org/10.2210/pdb5UBM/pdb

• Classification: IMMUNE SYSTEM/INHIBITOR
• Organism(s): Homo sapiens, Haementeria ghilianii
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2016-12-20 Released: 2017-11-08 
• Deposition Author(s): Pang, S.S., Whisstock, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.222 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 61.25 kDa 
• Atom Count: 3,936 
• Modelled Residue Count: 495 
• Deposited Residue Count: 541 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C1s subcomponent	A	252	Homo sapiens	Mutation(s): 0  EC: 3.4.21.42
UniProt & NIH Common Fund Data Resources
Find proteins for P09871 (Homo sapiens) Explore P09871  Go to UniProtKB:  P09871
PHAROS:  P09871 GTEx:  ENSG00000182326

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C1s subcomponent	B	152	Homo sapiens	Mutation(s): 0  EC: 3.4.21.42
UniProt & NIH Common Fund Data Resources
Find proteins for P09871 (Homo sapiens) Explore P09871  Go to UniProtKB:  P09871
PHAROS:  P09871 GTEx:  ENSG00000182326

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Gigastasin	C [auth I]	137	Haementeria ghilianii	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth C]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS	C [auth I]	L-PEPTIDE LINKING	C9 H11 N O6 S		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.222 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.35	α = 90
b = 89.35	β = 90
c = 146.871	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
Blu-Ice	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-08 
Deposition Author(s): Pang, S.S., Whisstock, J.C.

Revision History  

• Version 1.0: 2017-11-08
  Type: Initial release
  
• Version 1.1: 2017-11-29
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2023-11-15
  Changes: Data collection