› 5tzt

X-ray diffraction
2.89Å resolution

Crystal structure of human CD47 ECD bound to Fab of C47B161

Released:
DOI: 10.2210/pdb5tzt/pdb
PDB entry 5tzt coloured by chain, front view.
PDB entry 5tzt coloured by chain, side view.
PDB entry 5tzt coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Anti-leukemic activity and tolerability of anti-human CD47 monoclonal antibodies.
Pietsch EC, Dong J, Cardoso R, Zhang X, Chin D, Hawkins R, Dinh T, Zhou M, Strake B, Feng PH, Rocca M, Santos CD, Shan X, Danet-Desnoyers G, Shi F, Kaiser E, Millar HJ, Fenton S, Swanson R, Nemeth JA, Attar RM
Blood Cancer J 7 e536 (2017)
PMID: 28234345

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-231358 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Light Chain of Fab C47B161 Chains: B, L
Molecule details ›
Chains: B, L
Length: 219 amino acids
Theoretical weight: 24.14 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
Heavy Chain of Fab C47B161 Chains: A, H
Molecule details ›
Chains: A, H
Length: 226 amino acids
Theoretical weight: 24.31 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
Leukocyte surface antigen CD47 Chains: C, D
Molecule details ›
Chains: C, D
Length: 129 amino acids
Theoretical weight: 14.75 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q08722 (Residues: 19-141; Coverage: 40%)
Gene names: CD47, MER6
Sequence domains: CD47 immunoglobulin-like domain
Structure domains: Immunoglobulins

Ligands and Environments

2 bound ligands:
Ligand GOL 5 x GOL
Ligand NAG 3 x NAG
1 modified residue:
Ligand PCA 4 x PCA

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P21
Unit cell:
a: 74.569Å b: 60.974Å c: 124.133Å
α: 90° β: 90.05° γ: 90°
R-values:
R R work R free
0.261 0.257 0.328
Expression system: Homo sapiens

Quick links

Citations

23 review citations

Advances in Anti-Tumor Treatments Targeting the CD47/SIRPĪ± Axis.
Zhang et al. (2020)
22 more

5 mentions without citation

Macrophage checkpoint blockade: results from initial clinical trials, binding analyses, and CD47-SIRPĪ± structure-function.
Jalil et al. (2020)
4 more