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
- 4TY8
- Type
- protein
- Length
- 2,182 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyprotein
- UniProt
- D0PY27
- Ligands
- 3AV
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyprotein | protein | 544 | 48% helix, 16% strand | D0PY27 |
| B | Polyprotein | protein | 547 | 48% helix, 15% strand | D0PY27 |
| C | Polyprotein | protein | 545 | 48% helix, 15% strand | D0PY27 |
| D | Polyprotein | protein | 546 | 49% helix, 16% strand | D0PY27 |
Ligands and binding sites
- 3AV · 6-methyl-2H-chromen-2-one · ligand · 2 copies · chains A, B
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 | 998 | 0.80 | 0.82 | 88 | 3AV |
| 2 | 993 | 0.80 | 0.81 | 86 | 3AV |
| 3 | 940 | 0.79 | 0.81 | 85 | empty |
| 4 | 851 | 0.78 | 0.81 | 79 | empty |
| 5 | 909 | 0.74 | 0.78 | 86 | empty |
Interfaces
4 interfaces between chains.
- A–B · 605 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 259 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 56 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 12 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4TY8 · 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 4TY8 · PDBe 4TY8 · UniProt D0PY27
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