5TZT

Crystal structure of human CD47 ECD bound to Fab of C47B161


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.328
  • R-Value Work: 0.257

Literature

Macromolecules
Sequence Display for 5TZT

Classification: IMMUNE SYSTEM

Total Structure Weight: 127523.48

Macromolecule Entities
Molecule Chains Length Organism Details
Light Chain of Fab C47B161 B, L 219 Homo sapiens
Heavy Chain of Fab C47B161 A, H 226 Homo sapiens
Leukocyte surface antigen CD47 C, D 129 Homo sapiens Fragment: extracellular domain, UNP residues 19-141
Mutation: C15G
Details: Residue 1 is a Gln that cyclizes as pyroglutamate (PCA)
Gene Name(s): CD47 Gene View MER6
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

C, D N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B, H, L GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
PCA
Query on PCA
A, C, D, H L-PEPTIDE LINKING C5 H7 N O3 GLU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.328
  • R-Value Work: 0.257
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 74.57 α = 90.00
b = 60.97 β = 90.05
c = 124.13 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-11-22
  • Released Date: 2017-03-15
  • Deposition author(s): Cardoso, R.M.F.

Revision History

  • Version 1_0: 2017-03-15

    Type: Initial release