Research workbench
Phospholyase A1RDF1 from arthrobacter in complex with phosphoethanolamine
Analyse Phospholyase A1RDF1 from arthrobacter in complex with phosphoethanolamine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5G4J
- Type
- protein
- Length
- 845 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative aminotransferase class III protein
- EC
- 4.2.3.2
- UniProt
- A1RDF1
- Ligands
- EXT, NA
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative aminotransferase class III protein (EC 4.2.3.2) | protein | 423 | 40% helix, 18% strand | A1RDF1 |
| B | Putative aminotransferase class III protein (EC 4.2.3.2) | protein | 422 | 40% helix, 17% strand | A1RDF1 |
Ligands and binding sites
- EXT · {5-hydroxy-6-methyl-4-[(E)-{[2-(phosphonooxy)ethyl]imino}methyl]pyridin-3-yl}methyl dihydrogen phosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.75 | 0.97 | 19 | empty |
| 2 | 81 | 0.75 | 0.97 | 20 | empty |
| 3 | 487 | 0.74 | 0.83 | 49 | EXT |
| 4 | 472 | 0.73 | 0.82 | 48 | EXT |
| 5 | 185 | 0.53 | 0.79 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 4423 Ų buried · 64 hydrogen bonds · protein-protein
Compared structures
- 5G4J · Phospholyase A1RDF1 from Arthrobacter in complex with phosphoethanolamine · 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 A1RDF1
- Elsewhere: RCSB PDB 5G4J · PDBe 5G4J · UniProt A1RDF1
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