Research workbench
Crystal structure of human CD47 ecd bound to Fab of C47B161
Analyse Crystal structure of human CD47 ecd bound to Fab of C47B161 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TZT
- Type
- protein
- Length
- 1,096 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain of Fab C47B161; Heavy chain of Fab C47B161; Leukocyte surface antigen CD47
- UniProt
- Q08722
- Ligands
- NAG
- Pockets
- 17 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Light chain of Fab C47B161 | protein | 218 | 5% helix, 50% strand | — |
| A, H | Heavy chain of Fab C47B161 | protein | 217 | 7% helix, 52% strand | — |
| L | Light chain of Fab C47B161 | protein | 219 | 5% helix, 52% strand | — |
| C | Leukocyte surface antigen CD47 | protein | 111 | 14% helix, 39% strand | Q08722 |
| D | Leukocyte surface antigen CD47 | protein | 114 | 12% helix, 39% strand | Q08722 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains C, D
- GOL · Glycerol · additive · 5 copies · chains B, A, L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.73 | 0.96 | 30 | empty |
| 2 | 84 | 0.67 | 0.92 | 34 | empty |
| 3 | 52 | 0.66 | 0.95 | 19 | empty |
| 4 | 235 | 0.51 | 0.75 | 26 | empty |
| 5 | 291 | 0.49 | 0.73 | 52 | empty |
Interfaces
9 interfaces between chains.
- B–A · 1880 Ų buried · 12 hydrogen bonds · protein-protein
- L–H · 1859 Ų buried · 11 hydrogen bonds · protein-protein
- H–C · 431 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 414 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 294 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 4 modified, 3 glycan (disulfide, cyclization, N-glycosylation).
Compared structures
- 5TZT · Crystal structure of human CD47 ECD bound to Fab of C47B161 · 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 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 5TZT · PDBe 5TZT · UniProt Q08722
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