MolNFT v1 · #179831 · protein
Human gitr-gitrl complex
7KHD · Tumor necrosis factor ligand superfamily member 18: “Human gitr-gitrl complex”. X-ray diffraction, 1 ligand (NAG), 3 pockets (best druggability 0.37). MolNFT v1 #179831 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7KHD
- Type
- protein
- Length
- 438 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
- Q9UNG2, Q9Y5U5
- Ligands
- NAG
- Pockets
- 3 · best druggability 0.37
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tumor necrosis factor ligand superfamily member 18 | protein | 122 | 0% helix, 49% strand | Q9UNG2 |
| C | Tumor necrosis factor receptor superfamily member 18 | protein | 98 | 3% helix, 35% strand | Q9Y5U5 |
| D | Tumor necrosis factor receptor superfamily member 18 | protein | 96 | 4% helix, 34% strand | Q9Y5U5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.37 | 0.77 | 13 | empty |
| 2 | 73 | 0.30 | 0.73 | 18 | empty |
| 3 | 63 | 0.28 | 0.73 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–C · 396 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 390 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 390 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 349 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 14 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7KHD · Human GITR-GITRL complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UNG2 · AlphaFold monomer V2.0 prediction for tumor necrosis factor ligand superfamily member 18… · a predicted model of the same protein · chain A against A, TM-score 0.96
- Q9Y5U5 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member… · a predicted model of the same protein · chain C against A, TM-score 0.93
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 Q9UNG2
- Every structure of UniProt Q9Y5U5
- Elsewhere: RCSB PDB 7KHD · PDBe 7KHD · UniProt Q9UNG2 · UniProt Q9Y5U5
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