Research workbench
Crystal structure of murine gitr-gitrl complex
Analyse Crystal structure of murine gitr-gitrl complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E57
- Type
- protein
- Length
- 452 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, FUC
- Pockets
- 2 · best druggability 0.31
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor ligand superfamily member 18 | protein | 118 | 5% helix, 51% strand | Q7TS55 |
| B | Tumor necrosis factor ligand superfamily member 18 | protein | 123 | 2% helix, 46% strand | Q7TS55 |
| C | Tumor necrosis factor receptor superfamily member 18 | protein | 112 | 4% helix, 29% strand | O35714 |
| D | Tumor necrosis factor receptor superfamily member 18 | protein | 99 | 3% helix, 23% strand | O35714 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains D, C
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.31 | 0.72 | 17 | empty |
| 2 | 54 | 0.29 | 0.75 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1252 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 413 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 409 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7E57 · Crystal structure of murine GITR-GITRL complex · the same entry in another collection · chain D against D, 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 A against A, TM-score 0.98
- 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 0.87
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 7E57 · PDBe 7E57 · UniProt Q7TS55 · UniProt O35714
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