MolNFT v1 · #144327 · protein
Crystal structure of medicago truncatula thermospermine synthase (mttsps) in complex with spermidine
6BQ7: “Crystal structure of medicago truncatula thermospermine synthase (mttsps) in complex with spermidine”. X-ray diffraction, 1 ligand (SPD), 6 pockets (best druggability 0.84). MolNFT v1 #144327 on GenesisL1: 3D structure, binding…
- PDB
- 6BQ7
- Type
- protein
- Length
- 583 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thermospermine synthase
- UniProt
- G7K2D1
- Ligands
- SPD
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thermospermine synthase | protein | 292 | 35% helix, 33% strand | G7K2D1 |
| B | Thermospermine synthase | protein | 291 | 35% helix, 33% strand | G7K2D1 |
Ligands and binding sites
- SPD · Spermidine · ligand · 2 copies · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.84 | 0.96 | 36 | empty |
| 2 | 513 | 0.77 | 0.84 | 63 | SPD |
| 3 | 555 | 0.76 | 0.83 | 66 | SPD |
| 4 | 107 | 0.35 | 0.73 | 20 | empty |
| 5 | 68 | 0.30 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1703 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 6BQ7 · Crystal structure of Medicago truncatula Thermospermine Synthase (MtTSPS) in complex with… · 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 G7K2D1
- Elsewhere: RCSB PDB 6BQ7 · PDBe 6BQ7 · UniProt G7K2D1
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