3FBY

The crystal structure of the signature domain of cartilage oligomeric matrix protein.

• PDB DOI: https://doi.org/10.2210/pdb3FBY/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Drosophila
• Mutation(s): No 


• Deposited: 2008-11-20 Released: 2009-06-23 
• Deposition Author(s): Tan, K., Lawler, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 0.266 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 190.59 kDa 
• Atom Count: 12,777 
• Modelled Residue Count: 1,605 
• Deposited Residue Count: 1,653 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cartilage oligomeric matrix protein	A, B, C	551	Homo sapiens	Mutation(s): 0  Gene Names: COMP, COMP(cartilage oligomeric matrix protein)
UniProt & NIH Common Fund Data Resources
Find proteins for P49747 (Homo sapiens) Explore P49747  Go to UniProtKB:  P49747
PHAROS:  P49747 GTEx:  ENSG00000105664

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	D	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G04854NQ GlyCosmos:  G04854NQ GlyGen:  G04854NQ

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G62182OO GlyCosmos:  G62182OO GlyGen:  G62182OO

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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-glucopyranose	F	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21381MC GlyCosmos:  G21381MC GlyGen:  G21381MC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	KA [auth A], LA [auth A], MA [auth A], NA [auth A], OA [auth A], SB [auth B], TB [auth B], XC [auth C], YC [auth C], ZC [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	AA [auth A], AB [auth B], AC [auth C], BA [auth A], BB [auth B], BC [auth C], CA [auth A], CB [auth B], CC [auth C], DA [auth A], DB [auth B], DC [auth C], EA [auth A], EB [auth B], EC [auth C], FA [auth A], FB [auth B], FC [auth C], G [auth A], GA [auth A], GB [auth B], GC [auth C], H [auth A], HA [auth A], HB [auth B], HC [auth C], I [auth A], IA [auth A], IB [auth B], IC [auth C], J [auth A], JA [auth A], JB [auth B], JC [auth C], K [auth A], KB [auth B], KC [auth C], L [auth A], LB [auth B], LC [auth C], M [auth A], MB [auth B], MC [auth C], N [auth A], NB [auth B], NC [auth C], O [auth A], OB [auth B], OC [auth C], P [auth A], PA [auth B], PB [auth B], PC [auth C], Q [auth A], QA [auth B], QB [auth B], QC [auth C], R [auth A], RA [auth B], RB [auth B], RC [auth C], S [auth A], SA [auth B], SC [auth C], T [auth A], TA [auth B], TC [auth C], U [auth A], UA [auth B], UB [auth C], UC [auth C], V [auth A], VA [auth B], VB [auth C], VC [auth C], W [auth A], WA [auth B], WB [auth C], WC [auth C], X [auth A], XA [auth B], XB [auth C], Y [auth A], YA [auth B], YB [auth C], Z [auth A], ZA [auth B], ZB [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 0.266 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 192.242	α = 90
b = 192.242	β = 90
c = 145.681	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-23 
Deposition Author(s): Tan, K., Lawler, J.

Revision History  

• Version 1.0: 2009-06-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-09-06
  Changes: Data collection, Database references, Refinement description, Structure summary