Research workbench
Hapalindole U and dmspp bound AMBP3
Analyse Hapalindole U and dmspp bound AMBP3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y84
- Type
- protein
- Length
- 586 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AMBP3
- UniProt
- V5TDY7
- Ligands
- 8P6, DST
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | AMBP3 | protein | 293 | 36% helix, 26% strand | V5TDY7 |
Ligands and binding sites
- 8P6 · Hapalindole U · ligand · 2 copies · chains A, B
- DST · Dimethylallyl S-thiolodiphosphate · ligand · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 693 | 0.78 | 0.83 | 96 | 8P6, DST |
| 2 | 502 | 0.77 | 0.85 | 66 | 8P6, DST |
| 3 | 393 | 0.67 | 0.80 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 411 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5Y84 · Hapalindole U and DMSPP Bound AmbP3 · 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 V5TDY7
- Elsewhere: RCSB PDB 5Y84 · PDBe 5Y84 · UniProt V5TDY7
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