Research workbench
Computationally designed fentanyl binder - FEN49
Analyse Computationally designed fentanyl binder - FEN49 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TVY
- Type
- protein
- Length
- 374 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,4-beta-xylanase a
- EC
- 3.2.1.8
- UniProt
- P18429
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 63% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-1,4-beta-xylanase a (EC 3.2.1.8) | protein | 188 | 5% helix, 62% strand | P18429 |
| B | Endo-1,4-beta-xylanase a (EC 3.2.1.8) | protein | 186 | 5% helix, 63% strand | P18429 |
Ligands and binding sites
- XPE · 3,6,9,12,15,18,21,24,27-nonaoxanonacosane-1,29-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.65 | 0.83 | 28 | XPE |
| 2 | 239 | 0.64 | 0.82 | 35 | XPE |
| 3 | 120 | 0.36 | 0.73 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 410 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
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 P18429
- Elsewhere: RCSB PDB 5TVY · PDBe 5TVY · UniProt P18429
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