MolNFT v1 · #10316 · protein
Crystal structure of spermidine synthase from thermotoga maritima
1INL: “Crystal structure of spermidine synthase from thermotoga maritima”. X-ray diffraction, 12 pockets (best druggability 0.79). MolNFT v1 #10316 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1INL
- Type
- protein
- Length
- 1,151 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spermidine synthase
- EC
- 2.5.1.16
- UniProt
- Q9WZC2
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermidine synthase (EC 2.5.1.16) | protein | 285 | 32% helix, 31% strand | Q9WZC2 |
| B | Spermidine synthase (EC 2.5.1.16) | protein | 291 | 29% helix, 30% strand | Q9WZC2 |
| C | Spermidine synthase (EC 2.5.1.16) | protein | 293 | 31% helix, 29% strand | Q9WZC2 |
| D | Spermidine synthase (EC 2.5.1.16) | protein | 282 | 29% helix, 31% strand | Q9WZC2 |
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.79 | 0.99 | 20 | empty |
| 2 | 83 | 0.78 | 0.99 | 21 | empty |
| 3 | 409 | 0.66 | 0.79 | 46 | empty |
| 4 | 309 | 0.65 | 0.81 | 42 | empty |
| 5 | 358 | 0.64 | 0.79 | 49 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1940 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1905 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1667 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1573 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 59 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1INL · Crystal Structure of Spermidine Synthase from Thermotoga Maritima · the same entry in another collection · chain D against D, TM-score 1.00
- Q9WZC2 · AlphaFold monomer V2.0 prediction for polyamine aminopropyltransferase (Q9WZC2) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 Q9WZC2
- Elsewhere: RCSB PDB 1INL · PDBe 1INL · UniProt Q9WZC2
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