Research workbench
Crystal structure of TRIAMINE/AGMATINE aminopropyltransferase (spee) from thermus thermophilus, complexed with mta
Analyse Crystal structure of TRIAMINE/AGMATINE aminopropyltransferase (spee) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ANX
- Type
- protein
- Length
- 625 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spermidine synthase
- EC
- 2.5.1.16
- UniProt
- P83816
- Ligands
- MTA
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermidine synthase (EC 2.5.1.16) | protein | 312 | 31% helix, 31% strand | P83816 |
| B | Spermidine synthase (EC 2.5.1.16) | protein | 313 | 31% helix, 31% strand | P83816 |
Ligands and binding sites
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 470 | 0.78 | 0.86 | 66 | MTA |
| 2 | 530 | 0.78 | 0.85 | 59 | MTA |
| 3 | 69 | 0.72 | 0.97 | 16 | empty |
| 4 | 67 | 0.65 | 0.92 | 19 | empty |
| 5 | 82 | 0.31 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1853 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 3ANX · Crystal structure of triamine/agmatine aminopropyltransferase (SPEE) 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 P83816
- Elsewhere: RCSB PDB 3ANX · PDBe 3ANX · UniProt P83816
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