MolNFT v1 · #140322 · protein
Dmspp bound AMBP3
5Y72: “Dmspp bound AMBP3”. X-ray diffraction, 1 ligand (DST), 4 pockets (best druggability 0.79). MolNFT v1 #140322 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5Y72
- Type
- protein
- Length
- 587 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AMBP3
- UniProt
- V5TDY7
- Ligands
- DST
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | AMBP3 | protein | 294 | 37% helix, 29% strand | V5TDY7 |
| B | AMBP3 | protein | 293 | 37% helix, 28% strand | V5TDY7 |
Ligands and binding sites
- 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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1013 | 0.79 | 0.81 | 89 | DST |
| 2 | 470 | 0.76 | 0.84 | 59 | DST |
| 3 | 53 | 0.28 | 0.74 | 14 | empty |
| 4 | 54 | 0.27 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 342 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5Y72 · 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 5Y72 · PDBe 5Y72 · UniProt V5TDY7
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