Research workbench
Structure of the immunoglobulin-superfamily ectodomain of human CD47
Analyse Structure of the immunoglobulin-superfamily ectodomain of human CD47 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VSC
- Type
- protein
- Length
- 461 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leukocyte surface antigen CD47
- UniProt
- Q08722
- Ligands
- NAG, MG
- Pockets
- 1 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Leukocyte surface antigen CD47 | protein | 115 | 15% helix, 47% strand | Q08722 |
| D | Leukocyte surface antigen CD47 | protein | 116 | 15% helix, 47% strand | Q08722 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 173 | 0.55 | 0.80 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2552 Ų buried · 66 hydrogen bonds · protein-protein
- C–D · 2539 Ų buried · 60 hydrogen bonds · protein-protein
- B–C · 423 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 glycan, 4 disulfide, 4 modified (N-glycosylation, disulfide, cyclization).
Compared structures
- 2VSC · Structure of the immunoglobulin-superfamily ectodomain of human CD47 · the same entry in another collection · chain D against D, TM-score 1.00
- Q08722 · AlphaFold monomer V2.0 prediction for leukocyte surface antigen CD47 (Q08722) · a predicted model of the same protein · chain A against A, TM-score 0.87
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q08722
- Elsewhere: RCSB PDB 2VSC · PDBe 2VSC · UniProt Q08722
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