Research workbench
Structure of the signal-regulatory protein (sirp) alpha domain that binds CD47.
Analyse Structure of the signal-regulatory protein (sirp) alpha domain that binds CD47. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2UV3
- Type
- protein
- Length
- 242 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein phosphatase non-receptor type substrate 1
- UniProt
- P78324
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein phosphatase non-receptor type substrate 1 | protein | 120 | 3% helix, 41% strand | P78324 |
| B | Tyrosine-protein phosphatase non-receptor type substrate 1 | protein | 122 | 2% helix, 40% strand | P78324 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.57 | 0.83 | 28 | empty |
| 2 | 89 | 0.41 | 0.78 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 814 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2UV3 · Structure of the signal-regulatory protein (SIRP) alpha domain that binds CD47. · the same entry in another collection · chain A against A, TM-score 1.00
- P78324 · AlphaFold monomer V2.0 prediction for tyrosine-protein phosphatase non-receptor type… · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P78324
- Elsewhere: RCSB PDB 2UV3 · PDBe 2UV3 · UniProt P78324
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