MolNFT v1 · #182624 · protein
Structure of the full length 5-tm receptor CD47 bound to Fab B6H12
7MYZ · Fusion protein of leukocyte surface antigen CD47 an soluble…: “Structure of the full length 5-tm receptor CD47 bound to Fab B6H12”. X-ray diffraction, 1 ligand (NAG), 10 pockets (best druggability 0.70). MolNFT v1 #182624 on…
- PDB
- 7MYZ
- Type
- protein
- Length
- 1,234 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion protein of leukocyte surface antigen CD47 an soluble cytochrome B562; B6H12 Fab…
- UniProt
- Q08722
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Fusion protein of leukocyte surface antigen CD47 an soluble cytochrome B562 | protein | 263 | 46% helix, 19% strand | Q08722 |
| D | Fusion protein of leukocyte surface antigen CD47 an soluble cytochrome B562 | protein | 117 | 15% helix, 43% strand | Q08722 |
| H, I | B6H12 Fab heavy chain | protein | 214 | 8% helix, 52% strand | — |
| L, M | B6H12 Fab light chain | protein | 213 | 6% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains C, H, D, I
- GOL · Glycerol · additive · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1103 | 0.70 | 0.75 | 94 | GOL |
| 2 | 772 | 0.66 | 0.74 | 72 | empty |
| 3 | 169 | 0.55 | 0.80 | 23 | empty |
| 4 | 328 | 0.55 | 0.75 | 33 | empty |
| 5 | 115 | 0.38 | 0.74 | 23 | empty |
Interfaces
7 interfaces between chains.
- I–M · 1697 Ų buried · 13 hydrogen bonds · protein-protein
- H–L · 1697 Ų buried · 12 hydrogen bonds · protein-protein
- L–M · 888 Ų buried · 14 hydrogen bonds · protein-protein
- C–H · 623 Ų buried · 12 hydrogen bonds · protein-protein
- D–I · 619 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 7MYZ · Structure of the full length 5-TM receptor CD47 bound to Fab B6H12 · the same entry in another collection · chain M against M, TM-score 1.00
- Q08722 · AlphaFold monomer V2.0 prediction for leukocyte surface antigen CD47 (Q08722) · a predicted model of the same protein · chain D 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 7MYZ · PDBe 7MYZ · UniProt Q08722
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