Research workbench
Crystal structure of human CD47 ecd bound to Fab of B6H12.2
Analyse Crystal structure of human CD47 ecd bound to Fab of B6H12.2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TZU
- Type
- protein
- Length
- 542 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain of Fab B6H12.2; Heavy chain of Fab B6H12.2; Leukocyte surface antigen CD47
- UniProt
- Q08722
- Ligands
- NAG, BMA, MAN, SO4
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Light chain of Fab B6H12.2 | protein | 213 | 6% helix, 50% strand | — |
| H | Heavy chain of Fab B6H12.2 | protein | 214 | 8% helix, 51% strand | — |
| C | Leukocyte surface antigen CD47 | protein | 115 | 14% helix, 43% strand | Q08722 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains C, H
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- SO4 · Sulfate ion · ion · 2 copies · chains L, H
- ACT · Acetate ion · additive · 3 copies · chains H, C
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 611 | 0.64 | 0.75 | 59 | empty |
| 2 | 66 | 0.32 | 0.75 | 15 | empty |
| 3 | 81 | 0.31 | 0.73 | 22 | empty |
| 4 | 56 | 0.29 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1609 Ų buried · 17 hydrogen bonds · protein-protein
- H–C · 607 Ų buried · 12 hydrogen bonds · protein-protein
- L–C · 444 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 5TZU · Crystal structure of human CD47 ECD bound to Fab of B6H12.2 · the same entry in another collection · chain L against L, TM-score 1.00
- Q08722 · AlphaFold monomer V2.0 prediction for leukocyte surface antigen CD47 (Q08722) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 5TZU · PDBe 5TZU · UniProt Q08722
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