Research workbench
Crystal structure of medicago truncatula thermospermine synthase (mttsps) in complex with adenosine
Analyse Crystal structure of medicago truncatula thermospermine synthase (mttsps) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BQ4
- Type
- protein
- Length
- 584 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thermospermine synthase acaulis protein
- UniProt
- G7K2D1
- Ligands
- ADN
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thermospermine synthase acaulis protein | protein | 292 | 35% helix, 33% strand | G7K2D1 |
Ligands and binding sites
- ADN · Adenosine · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 267 | 0.85 | 0.96 | 35 | empty |
| 2 | 574 | 0.78 | 0.84 | 57 | ADN, B3P, GOL |
| 3 | 581 | 0.76 | 0.82 | 59 | ADN, MES, GOL |
| 4 | 56 | 0.43 | 0.83 | 17 | empty |
| 5 | 83 | 0.31 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1688 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 6BQ4 · 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 6BQ4 · PDBe 6BQ4 · UniProt G7K2D1
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