Research workbench
Human TNFRSF25 death domain
Analyse Human TNFRSF25 death domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YGS
- Type
- protein
- Length
- 1,827 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human TNRSF25 death domain
- Ligands
- GLC, SO4
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Human TNRSF25 death domain | protein | 456 | 50% helix, 16% strand | — |
| B | Human TNRSF25 death domain | protein | 456 | 50% helix, 17% strand | — |
| C | Human TNRSF25 death domain | protein | 457 | 51% helix, 16% strand | — |
| D | Human TNRSF25 death domain | protein | 458 | 51% helix, 17% strand | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 12 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 20 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.75 | 0.85 | 31 | GLC |
| 2 | 394 | 0.74 | 0.84 | 30 | GLC |
| 3 | 700 | 0.74 | 0.80 | 85 | SO4 |
| 4 | 387 | 0.73 | 0.83 | 35 | GLC |
| 5 | 379 | 0.72 | 0.83 | 34 | GLC |
Interfaces
4 interfaces between chains.
- C–D · 1407 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1311 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 812 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 796 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5YGS · Human TNFRSF25 death domain · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 5YGS · PDBe 5YGS
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