Research workbench
Human TNFRSF25 death domain mutant-D412E
Analyse Human TNFRSF25 death domain mutant-D412E in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YGP
- Type
- protein
- Length
- 1,812 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TNFRSF25 death domain
- Ligands
- GLC, SO4
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | TNFRSF25 death domain | protein | 453 | 51% helix, 17% strand | — |
| C | TNFRSF25 death domain | protein | 452 | 50% helix, 17% strand | — |
| D | TNFRSF25 death domain | protein | 454 | 51% helix, 17% strand | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 436 | 0.75 | 0.84 | 49 | GLC |
| 2 | 777 | 0.75 | 0.80 | 91 | empty |
| 3 | 315 | 0.72 | 0.84 | 29 | GLC |
| 4 | 347 | 0.71 | 0.84 | 38 | GLC |
| 5 | 368 | 0.69 | 0.82 | 38 | GLC |
Interfaces
4 interfaces between chains.
- C–D · 1379 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1310 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 851 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 849 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5YGP · Human TNFRSF25 death domain mutant-D412E · 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 5YGP · PDBe 5YGP
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