6HG7

Crystal structure of a collagen II fragment containing the binding site of PEDF and COMP, (POG)4-LKG HRG FTG LQG-POG(4)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

COMP and TSP-4 interact specifically with the novel GXKGHR motif only found in fibrillar collagens.

Gebauer, J.M.Kohler, A.Dietmar, H.Gompert, M.Neundorf, I.Zaucke, F.Koch, M.Baumann, U.

(2018) Sci Rep 8: 17187-17187


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
collagen-like peptide
A, B, C
37N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NH2
Query on NH2

Download SDF File 
Download CCD File 
A, B, C
AMINO GROUP
H2 N
QGZKDVFQNNGYKY-UHFFFAOYAF
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
HYP
Query on HYP
A, B, C
L-PEPTIDE LINKINGC5 H9 N O3PRO
ACE
Query on ACE
A, B, C
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.152 
  • Space Group: I 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 31.970α = 90.00
b = 23.640β = 92.70
c = 107.939γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
MOSFLMdata reduction
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB829/B11

Revision History 

  • Version 1.0: 2018-12-05
    Type: Initial release