Research workbench
Computationally designed fentanyl binder - FEN49* apo
Analyse Computationally designed fentanyl binder - FEN49* apo in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TVV
- Type
- protein
- Length
- 554 residues
- Chains
- 3
- 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
- Ligands
- K
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 65% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endo-1,4-beta-xylanase a (EC 3.2.1.8) | protein | 185 | 5% helix, 66% strand | P18429 |
| C | Endo-1,4-beta-xylanase a (EC 3.2.1.8) | protein | 184 | 5% helix, 64% strand | P18429 |
Ligands and binding sites
- K · Potassium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.77 | 0.79 | 79 | empty |
| 2 | 610 | 0.67 | 0.77 | 54 | empty |
| 3 | 273 | 0.58 | 0.77 | 33 | empty |
| 4 | 69 | 0.34 | 0.77 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 480 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 405 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 14 Ų buried · 0 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 5TVV · PDBe 5TVV · UniProt P18429
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