MolNFT v1 · #179851 · protein
Mouse gitr-gitrl complex
7KHX · Tumor necrosis factor ligand superfamily member 18: “Mouse gitr-gitrl complex”. X-ray diffraction, 1 ligand (NAG), 4 pockets (best druggability 0.37). MolNFT v1 #179851 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7KHX
- Type
- protein
- Length
- 459 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor ligand superfamily member 18; Tumor necrosis factor receptor…
- UniProt
- Q7TS55, O35714
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.37
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Tumor necrosis factor ligand superfamily member 18 | protein | 124 | 2% helix, 43% strand | Q7TS55 |
| D | Tumor necrosis factor receptor superfamily member 18 | protein | 107 | 4% helix, 25% strand | O35714 |
| C | Tumor necrosis factor receptor superfamily member 18 | protein | 104 | 4% helix, 29% strand | O35714 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.37 | 0.75 | 19 | empty |
| 2 | 94 | 0.37 | 0.75 | 19 | empty |
| 3 | 93 | 0.36 | 0.74 | 17 | empty |
| 4 | 70 | 0.35 | 0.76 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–A · 1506 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 414 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 358 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7KHX · Mouse GITR-GITRL complex · the same entry in another collection · chain B against B, TM-score 1.00
- Q7TS55 · AlphaFold monomer V2.0 prediction for tumor necrosis factor ligand superfamily member 18… · a predicted model of the same protein · chain B against A, TM-score 0.97
- O35714 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member… · a predicted model of the same protein · chain D against A, TM-score 0.86
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 Q7TS55
- Every structure of UniProt O35714
- Elsewhere: RCSB PDB 7KHX · PDBe 7KHX · UniProt Q7TS55 · UniProt O35714
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