MolNFT v1 · #18433 · protein
SPERMIDINE/PUTRESCINE-binding protein complexed with spermidine (dimer form)
1POY: “SPERMIDINE/PUTRESCINE-binding protein complexed with spermidine (dimer form)”. X-ray diffraction, 1 ligand (SPD), 18 pockets (best druggability 0.82). MolNFT v1 #18433 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1POY
- Type
- protein
- Length
- 1,292 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SPERMIDINE/PUTRESCINE-binding protein
- UniProt
- P23861
- Ligands
- SPD
- Pockets
- 18 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1, 2, 3, 4 | SPERMIDINE/PUTRESCINE-binding protein | protein | 323 | 41% helix, 19% strand | P23861 |
Ligands and binding sites
- SPD · Spermidine · ligand · 4 copies · chains 1, 2, 3, 4
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.82 | 0.86 | 50 | empty |
| 2 | 602 | 0.80 | 0.85 | 49 | empty |
| 3 | 181 | 0.56 | 0.80 | 42 | empty |
| 4 | 69 | 0.55 | 0.88 | 22 | empty |
| 5 | 51 | 0.52 | 0.89 | 19 | empty |
Interfaces
2 interfaces between chains.
- 3–4 · 1141 Ų buried · 16 hydrogen bonds · protein-protein
- 1–2 · 1112 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 1POY · SPERMIDINE/PUTRESCINE-binding protein complexed with spermidine (dimer form) · the same entry in another collection · chain 1 against 1, 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 P23861
- Elsewhere: RCSB PDB 1POY · PDBe 1POY · UniProt P23861
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