MolNFT v1 · #153067 · protein
Crystal structure of the branched-chain polyamine synthase from thermus thermophilus (tth-bpsa) in complex with N4- aminopropylspermidine and 5'-methylthioadenosine
6J27 · N(4)-BIS(AMINOPROPYL)SPERMIDINE synthase: “Crystal structure of the branched-chain polyamine synthase from thermus thermophilus (tth-bpsa) in complex…”. X-ray diffraction, 3 ligands (MTA, N4P, FE), 14 pockets (best druggability…
- PDB
- 6J27
- Type
- protein
- Length
- 1,375 residues
- Chains
- 4
- 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
- Q72L89
- Ligands
- MTA, N4P, FE
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | N(4)-BIS(AMINOPROPYL)SPERMIDINE synthase (EC 2.5.1.128) | protein | 344 | 40% helix, 17% strand | Q72L89 |
| C | N(4)-BIS(AMINOPROPYL)SPERMIDINE synthase (EC 2.5.1.128) | protein | 343 | 38% helix, 17% strand | Q72L89 |
Ligands and binding sites
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 4 copies · chains A, B, C, D
- N4P · N,N-bis(3-aminopropyl)butane-1,4-diamine · ligand · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 2 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 9 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 848 | 0.80 | 0.83 | 76 | PEG |
| 2 | 852 | 0.80 | 0.83 | 87 | PEG |
| 3 | 247 | 0.77 | 0.91 | 42 | MTA, N4P |
| 4 | 241 | 0.77 | 0.90 | 39 | MTA, N4P |
| 5 | 260 | 0.76 | 0.90 | 44 | MTA, N4P |
Interfaces
5 interfaces between chains.
- A–B · 2441 Ų buried · 54 hydrogen bonds · protein-protein
- C–D · 2438 Ų buried · 64 hydrogen bonds · protein-protein
- B–D · 591 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 401 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 156 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6J27 · Crystal structure of the branched-chain polyamine synthase from Thermus thermophilus… · 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 Q72L89
- Elsewhere: RCSB PDB 6J27 · PDBe 6J27 · UniProt Q72L89
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.