Research workbench
An ligand-observed mass spectrometry-based approach integrated into the fragment based lead discovery pipeline
Analyse An ligand-observed mass spectrometry-based approach integrated into the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TYB
- Type
- protein
- Length
- 2,179 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyprotein
- EC
- 2.7.7.48
- UniProt
- D0PY27
- Ligands
- 3B1
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Polyprotein (EC 2.7.7.48) | protein | 545 | 48% helix, 16% strand | D0PY27 |
| B | Polyprotein (EC 2.7.7.48) | protein | 544 | 49% helix, 16% strand | D0PY27 |
Ligands and binding sites
- 3B1 · (2R)-morpholin-4-yl(phenyl)ethanenitrile · ligand · 4 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 922 | 0.79 | 0.81 | 81 | 3B1 |
| 2 | 951 | 0.79 | 0.81 | 87 | 3B1 |
| 3 | 902 | 0.79 | 0.81 | 79 | 3B1 |
| 4 | 817 | 0.77 | 0.81 | 71 | 3B1 |
| 5 | 805 | 0.72 | 0.78 | 78 | empty |
Interfaces
3 interfaces between chains.
- A–B · 579 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 278 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 20 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4TYB · An Ligand-observed Mass Spectrometry-based Approach Integrated into the Fragment Based… · 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
- Every structure of UniProt D0PY27
- Elsewhere: RCSB PDB 4TYB · PDBe 4TYB · UniProt D0PY27
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