Research workbench
Hapalindole a and dmspp bound AMBP3
Analyse Hapalindole a 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
- 5Y7C
- Type
- protein
- Length
- 583 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AMBP3
- UniProt
- V5TDY7
- Ligands
- DST, 8O0
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | AMBP3 | protein | 291 | 37% helix, 26% strand | V5TDY7 |
| B | AMBP3 | protein | 292 | 37% helix, 26% strand | V5TDY7 |
Ligands and binding sites
- DST · Dimethylallyl S-thiolodiphosphate · ligand · 2 copies · chains A, B
- 8O0 · Hapalindole A · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 478 | 0.79 | 0.87 | 54 | DST, 8O0 |
| 2 | 1141 | 0.78 | 0.80 | 103 | DST, 8O0 |
Interfaces
1 interface between chains.
- A–B · 324 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5Y7C · Hapalindole A 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 5Y7C · PDBe 5Y7C · UniProt V5TDY7
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