MolNFT v1 · #147130 · protein
Interferon gamma signalling complex with IFNGR1 and IFNGR2
6E3L: “Interferon gamma signalling complex with IFNGR1 and IFNGR2”. X-ray diffraction, 4 ligands (CYS, NAG, BMA), 10 pockets (best druggability 0.76). MolNFT v1 #147130 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6E3L
- Type
- protein
- Length
- 1,083 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interferon gamma; Interferon gamma receptor 1; Interferon gamma receptor 2
- UniProt
- P01579, P15260, P38484
- Ligands
- CYS, NAG, BMA, MAN
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interferon gamma | protein | 125 | 66% helix, 0% strand | P01579 |
| B | Interferon gamma | protein | 126 | 66% helix, 0% strand | P01579 |
| C | Interferon gamma receptor 1 | protein | 204 | 3% helix, 50% strand | P15260 |
| D | Interferon gamma receptor 1 | protein | 202 | 3% helix, 50% strand | P15260 |
| E, I | Interferon gamma receptor 2 | protein | 213 | 2% helix, 47% strand | P38484 |
Ligands and binding sites
- CYS · Cysteine · ligand · 2 copies · chains E, I
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains C, D, E, B, I, A
- BMA · beta-D-mannopyranose · sugar · 4 copies
- MAN · alpha-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 856 | 0.76 | 0.80 | 81 | empty |
| 2 | 615 | 0.74 | 0.81 | 77 | empty |
| 3 | 411 | 0.63 | 0.78 | 44 | empty |
| 4 | 351 | 0.62 | 0.78 | 45 | empty |
| 5 | 284 | 0.61 | 0.79 | 35 | empty |
Interfaces
10 interfaces between chains.
- A–B · 3994 Ų buried · 40 hydrogen bonds · protein-protein
- C–I · 870 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 813 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 804 Ų buried · 10 hydrogen bonds · protein-protein
- A–I · 799 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 12 glycan, 2 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 6E3L · Interferon gamma signalling complex with IFNGR1 and IFNGR2 · the same entry in another collection · chain I against I, TM-score 1.00
- P15260 · AlphaFold monomer V2.0 prediction for interferon gamma receptor 1 (P15260) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P01579 · AlphaFold monomer V2.0 prediction for interferon gamma (P01579) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P38484 · AlphaFold monomer V2.0 prediction for interferon gamma receptor 2 (P38484) · a predicted model of the same protein · chain I 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 P01579
- Every structure of UniProt P15260
- Every structure of UniProt P38484
- Elsewhere: RCSB PDB 6E3L · PDBe 6E3L · UniProt P01579 · UniProt P15260 · UniProt P38484
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