Research workbench
Crystal structure of the branched-chain polyamine synthase (bpsa) from thermococcus kodakarensis
Analyse Crystal structure of the branched-chain polyamine synthase (bpsa) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XNF
- Type
- protein
- Length
- 700 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
- FE, SO4
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N(4)-BIS(AMINOPROPYL)SPERMIDINE synthase (EC 2.5.1.128) | protein | 350 | 40% helix, 16% strand | Q5JIZ3 |
Ligands and binding sites
- FE · Fe (III) ion · metal · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 568 | 0.71 | 0.79 | 73 | empty |
| 2 | 446 | 0.68 | 0.79 | 56 | empty |
| 3 | 143 | 0.55 | 0.81 | 28 | GOL |
| 4 | 132 | 0.54 | 0.82 | 31 | empty |
| 5 | 85 | 0.49 | 0.83 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 2476 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 5XNF · Crystal structure of the branched-chain polyamine synthase (BpsA) from Thermococcus… · 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 B against A, TM-score 0.96
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 5XNF · PDBe 5XNF · UniProt Q5JIZ3
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