MolNFT v1 · #139697 · protein
Crystal structure of the branched-chain polyamine synthase (bpsa) in complex with spermidine
5XNH · N(4)-BIS(AMINOPROPYL)SPERMIDINE synthase: “Crystal structure of the branched-chain polyamine synthase (bpsa) in complex with spermidine”. X-ray diffraction, 2 ligands (SPD, FE), 6 pockets (best druggability 0.74). MolNFT v1 #139697…
- PDB
- 5XNH
- Type
- protein
- Length
- 678 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N(4)-BIS(AMINOPROPYL)SPERMIDINE synthase
- EC
- 2.5.1.128
- UniProt
- Q5JIZ3
- Ligands
- SPD, FE
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N(4)-BIS(AMINOPROPYL)SPERMIDINE synthase (EC 2.5.1.128) | protein | 340 | 41% helix, 17% strand | Q5JIZ3 |
| H | N(4)-BIS(AMINOPROPYL)SPERMIDINE synthase (EC 2.5.1.128) | protein | 338 | 42% helix, 17% strand | Q5JIZ3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 281 | 0.74 | 0.87 | 48 | SPD |
| 2 | 278 | 0.70 | 0.85 | 46 | SPD |
| 3 | 96 | 0.46 | 0.81 | 26 | empty |
| 4 | 109 | 0.46 | 0.79 | 26 | empty |
| 5 | 100 | 0.43 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–H · 2529 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 5XNH · Crystal structure of the branched-chain polyamine synthase (BpsA) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5JIZ3 · AlphaFold monomer V2.0 prediction for N(4)-BIS(AMINOPROPYL)SPERMIDINE synthase (Q5JIZ3) · a predicted model of the same protein · chain H against A, TM-score 0.99
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 Q5JIZ3
- Elsewhere: RCSB PDB 5XNH · PDBe 5XNH · UniProt Q5JIZ3
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