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Crystal structure of the aminopropyltransferase, spee from hyperthermophilic crenarchaeon, pyrobaculum calidifontis in complex with 5'-methylthioadenosine (mta) and spermidine
Analyse Crystal structure of the aminopropyltransferase, spee from hyperthermophilic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XIH
- Type
- protein
- Length
- 575 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyamine aminopropyltransferase
- EC
- 2.5.1.16
- UniProt
- A3MU81
- Ligands
- MTA, SPD
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyamine aminopropyltransferase (EC 2.5.1.16) | protein | 288 | 35% helix, 31% strand | A3MU81 |
| B | Polyamine aminopropyltransferase (EC 2.5.1.16) | protein | 287 | 35% helix, 31% strand | A3MU81 |
Ligands and binding sites
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 2 copies · chains A, B
- SPD · Spermidine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.78 | 0.96 | 37 | MTA, SPD |
| 2 | 122 | 0.77 | 0.96 | 36 | MTA, SPD |
| 3 | 76 | 0.74 | 0.97 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2446 Ų buried · 48 hydrogen bonds · protein-protein
Compared structures
- 7XIH · Crystal structure of the aminopropyltransferase, SpeE from hyperthermophilic… · the same entry in another collection · chain A against A, TM-score 1.00
- A3MU81 · AlphaFold monomer V2.0 prediction for polyamine aminopropyltransferase (A3MU81) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 A3MU81
- Elsewhere: RCSB PDB 7XIH · PDBe 7XIH · UniProt A3MU81
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