Research workbench
Crystal structure of human CD47 ecd bound to Fab of C47B222
Analyse Crystal structure of human CD47 ecd bound to Fab of C47B222 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TZ2
- Type
- protein
- Length
- 539 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C47B222 Fab heavy chain; C47B222 Fab light chain; Leukocyte surface antigen CD47
- UniProt
- Q08722
- Ligands
- NAG
- Pockets
- 3 · best druggability 0.50
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | C47B222 Fab heavy chain | protein | 213 | 6% helix, 54% strand | — |
| L | C47B222 Fab light chain | protein | 212 | 5% helix, 50% strand | — |
| C | Leukocyte surface antigen CD47 | protein | 114 | 14% helix, 47% strand | Q08722 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains C
- GOL · Glycerol · additive · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.50 | 0.74 | 38 | empty |
| 2 | 66 | 0.31 | 0.75 | 17 | empty |
| 3 | 82 | 0.30 | 0.72 | 21 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1750 Ų buried · 13 hydrogen bonds · protein-protein
- H–C · 524 Ų buried · 11 hydrogen bonds · protein-protein
- L–C · 313 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 5TZ2 · Crystal structure of human CD47 ECD bound to Fab of C47B222 · the same entry in another collection · chain H against H, 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 0.99
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 5TZ2 · PDBe 5TZ2 · UniProt Q08722
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