Research workbench
Crystal structure of the aminopropyltransferase, spee from hyperthermophilic crenarchaeon, pyrobaculum calidifontis in complex with 5'-methylthioadenosine (mta) & aminopropylagmatine
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
- 7XII
- Type
- protein
- Length
- 1,148 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyamine aminopropyltransferase
- EC
- 2.5.1.16
- UniProt
- A3MU81
- Ligands
- MTA, AG3
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Polyamine aminopropyltransferase (EC 2.5.1.16) | protein | 286 | 35% helix, 31% strand | A3MU81 |
| B, D | Polyamine aminopropyltransferase (EC 2.5.1.16) | protein | 288 | 35% helix, 31% strand | A3MU81 |
Ligands and binding sites
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 4 copies · chains A, B, C, D
- AG3 · 1-{4-[(3-aminopropyl)amino]butyl}guanidine · ligand · 4 copies · chains A, B, C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.79 | 0.97 | 36 | MTA, AG3 |
| 2 | 115 | 0.78 | 0.97 | 36 | MTA, AG3 |
| 3 | 120 | 0.77 | 0.96 | 35 | MTA, AG3 |
| 4 | 82 | 0.75 | 0.97 | 19 | empty |
| 5 | 78 | 0.73 | 0.96 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2411 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 2410 Ų buried · 44 hydrogen bonds · protein-protein
- A–C · 144 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 135 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 94 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7XII · Crystal structure of the aminopropyltransferase, SpeE from hyperthermophilic… · the same entry in another collection · chain B against B, TM-score 1.00
- A3MU81 · AlphaFold monomer V2.0 prediction for polyamine aminopropyltransferase (A3MU81) · a predicted model of the same protein · chain A 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 7XII · PDBe 7XII · UniProt A3MU81
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