MolNFT v1 · #153068 · protein
Crystal structure of the branched-chain polyamine synthase C9 mutein from thermus thermophilus (tth-bpsa C9) in complex with N4- aminopropylspermidine and 5'-methylthioadenosine
6J28 · N(4)-BIS(AMINOPROPYL)SPERMIDINE synthase: “Crystal structure of the branched-chain polyamine synthase C9 mutein from thermus thermophilus (tth-bpsa C9)…”. X-ray diffraction, 3 ligands (N4P, MTA, FE), 20 pockets (best druggability…
- PDB
- 6J28
- Type
- protein
- Length
- 1,380 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
- N4P, MTA, FE
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | N(4)-BIS(AMINOPROPYL)SPERMIDINE synthase (EC 2.5.1.128) | protein | 345 | 38% helix, 17% strand | Q72L89 |
Ligands and binding sites
- N4P · N,N-bis(3-aminopropyl)butane-1,4-diamine · ligand · 4 copies · chains A, B, C, D
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 2 copies · chains A, C, B, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1020 | 0.85 | 0.87 | 111 | MES |
| 2 | 193 | 0.82 | 0.96 | 42 | N4P, MTA |
| 3 | 168 | 0.81 | 0.96 | 38 | N4P, MTA |
| 4 | 172 | 0.80 | 0.96 | 40 | N4P, MTA |
| 5 | 184 | 0.80 | 0.95 | 40 | N4P, MTA |
Interfaces
5 interfaces between chains.
- B–D · 2427 Ų buried · 55 hydrogen bonds · protein-protein
- A–C · 2390 Ų buried · 52 hydrogen bonds · protein-protein
- B–C · 581 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 431 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 146 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6J28 · Crystal structure of the branched-chain polyamine synthase C9 mutein from Thermus… · 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 6J28 · PDBe 6J28 · UniProt Q72L89
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