MolNFT v1 · #66179 · protein
Crystal structure of saporin-L1 in complex with the dinucleotide inhibitor, a transition state analogue
3HIT · Vacuolar saporin: “Crystal structure of saporin-L1 in complex with the dinucleotide inhibitor, a transition state analogue”. X-ray diffraction, 1 ligand (DYN), 5 pockets (best druggability 0.69). MolNFT v1 #66179 on GenesisL1: 3D…
- PDB
- 3HIT
- Type
- protein
- Length
- 514 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar saporin
- EC
- 3.2.2.22
- UniProt
- Q2QEH4
- Ligands
- DYN
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Vacuolar saporin (EC 3.2.2.22) | protein | 257 | 37% helix, 22% strand | Q2QEH4 |
Ligands and binding sites
- DYN · 5'-O-[(S)-{[(3R,4R)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-({[(S)-hydroxy(3-hydroxypropoxy)phosphoryl]oxy}methyl)pyrrolidin-3-yl]oxy}(hydroxy)phosphoryl]-3'-O-[(R)-hydroxy(4-hydroxybutoxy)phosphoryl]-2'-O-methylguanosine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.69 | 0.80 | 44 | empty |
| 2 | 280 | 0.59 | 0.78 | 37 | empty |
| 3 | 95 | 0.48 | 0.81 | 22 | DYN |
| 4 | 89 | 0.48 | 0.81 | 21 | DYN |
| 5 | 61 | 0.43 | 0.82 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 701 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3HIT · Crystal structure of Saporin-L1 in complex with the dinucleotide inhibitor, a transition… · 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 Q2QEH4
- Elsewhere: RCSB PDB 3HIT · PDBe 3HIT · UniProt Q2QEH4
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