Research workbench
Crystal structure of signal regulatory protein gamma (sirp-gamma) in complex with FABOX117
Analyse Crystal structure of signal regulatory protein gamma (sirp-gamma) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I2X
- Type
- protein
- Length
- 1,486 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FABOX117 light chain; FABOX117 heavy chain; Signal-regulatory protein gamma
- UniProt
- Q9P1W8
- Ligands
- NAG, ZN, CL
- Pockets
- 16 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | FABOX117 light chain | protein | 214 | 7% helix, 55% strand | — |
| B | FABOX117 heavy chain | protein | 229 | 9% helix, 50% strand | — |
| D | FABOX117 heavy chain | protein | 219 | 7% helix, 50% strand | — |
| E | Signal-regulatory protein gamma | protein | 314 | 2% helix, 52% strand | Q9P1W8 |
| F | Signal-regulatory protein gamma | protein | 296 | 4% helix, 51% strand | Q9P1W8 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains E, F
- ZN · Zinc ion · metal · chains B
- CL · Chloride ion · ion · 2 copies · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 504 | 0.68 | 0.79 | 61 | empty |
| 2 | 502 | 0.67 | 0.78 | 58 | empty |
| 3 | 416 | 0.65 | 0.79 | 59 | empty |
| 4 | 586 | 0.62 | 0.74 | 68 | empty |
| 5 | 369 | 0.61 | 0.77 | 55 | empty |
Interfaces
9 interfaces between chains.
- A–B · 2090 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1984 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1214 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 830 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 817 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4I2X · Crystal structure of Signal Regulatory Protein gamma (SIRP-gamma) in complex with FabOX117 · the same entry in another collection · chain F against F, TM-score 1.00
- Q9P1W8 · AlphaFold monomer V2.0 prediction for signal-regulatory protein gamma (Q9P1W8) · a predicted model of the same protein · chain E 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 Q9P1W8
- Elsewhere: RCSB PDB 4I2X · PDBe 4I2X · UniProt Q9P1W8
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