Research workbench
AzeJ in complex with MTA and AZE from Pseudomonas aeruginosa (P4(2)22)
Analyse AzeJ in complex with MTA and AZE from Pseudomonas aeruginosa (P4(2)22) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8RYF
- Type
- protein
- Length
- 453 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.95
- Source
- Pseudomonas aeruginosa
- Molecule
- Class I SAM-dependent methyltransferase
- UniProt
- Q9HYR0
- Ligands
- MTA, 02A, NA, PO4
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · resolution 1.95 · 2 distinct chains · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Class I SAM-dependent methyltransferase | protein | 232 | 40% helix, 25% strand | Q9HYR0 |
| B | Class I SAM-dependent methyltransferase | protein | 221 | 39% helix, 24% strand | Q9HYR0 |
Ligands and binding sites
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 2 copies · chains A, B
- 02A · (2S)-azetidine-2-carboxylic acid · ligand · chains A
- NA · Sodium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
- GOL · Glycerol · additive · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.80 | 0.97 | 32 | GOL |
| 2 | 119 | 0.78 | 0.96 | 26 | MTA, 02A |
| 3 | 239 | 0.53 | 0.76 | 25 | MTA |
| 4 | 79 | 0.39 | 0.78 | 23 | empty |
| 5 | 65 | 0.38 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1592 Ų buried · 22 hydrogen bonds · protein-protein
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 Q9HYR0
- Elsewhere: RCSB PDB 8RYF · PDBe 8RYF · UniProt Q9HYR0
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