Research workbench
Structure of human CD47 in complex with human signal regulatory protein (sirp) alpha
Analyse Structure of human CD47 in complex with human signal regulatory protein (sirp)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JJT
- Type
- protein
- Length
- 457 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein phosphatase non-receptor type substrate 1; Leukocyte surface antigen CD47
- UniProt
- P78324, Q08722
- Ligands
- NAG
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein phosphatase non-receptor type substrate 1 | protein | 113 | 3% helix, 42% strand | P78324 |
| B | Tyrosine-protein phosphatase non-receptor type substrate 1 | protein | 114 | 3% helix, 42% strand | P78324 |
| C, D | Leukocyte surface antigen CD47 | protein | 115 | 15% helix, 46% strand | Q08722 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains C, B, D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 565 | 0.75 | 0.83 | 61 | empty |
| 2 | 553 | 0.75 | 0.82 | 56 | NAG |
| 3 | 279 | 0.65 | 0.81 | 28 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1027 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 995 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 563 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 135 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 122 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 4 disulfide, 2 modified (N-glycosylation, disulfide, cyclization).
Compared structures
- 2JJT · Structure of human CD47 in complex with human signal regulatory protein (SIRP) alpha · 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 D against A, TM-score 0.99
- P78324 · AlphaFold monomer V2.0 prediction for tyrosine-protein phosphatase non-receptor type… · a predicted model of the same protein · chain A against A, TM-score 0.96
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
- Every structure of UniProt Q08722
- Elsewhere: RCSB PDB 2JJT · PDBe 2JJT · UniProt P78324 · UniProt Q08722
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