MolNFT v1 · #119711 · protein
Plp-dependent phospholyase A1RDF1 from arthrobacter aurescens TC1
5G4I: “Plp-dependent phospholyase A1RDF1 from arthrobacter aurescens TC1”. X-ray diffraction, 2 ligands (PLP, PO4), 9 pockets (best druggability 0.76). MolNFT v1 #119711 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5G4I
- Type
- protein
- Length
- 845 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholyase
- EC
- 4.2.3.2
- UniProt
- A1RDF1
- Ligands
- PLP, PO4
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholyase (EC 4.2.3.2) | protein | 423 | 40% helix, 17% strand | A1RDF1 |
| B | Phospholyase (EC 4.2.3.2) | protein | 422 | 40% helix, 17% strand | A1RDF1 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 5 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
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 | 93 | 0.76 | 0.97 | 21 | empty |
| 2 | 523 | 0.75 | 0.83 | 52 | PLP, PO4 |
| 3 | 98 | 0.74 | 0.95 | 21 | empty |
| 4 | 523 | 0.74 | 0.82 | 49 | PLP, PO4 |
| 5 | 202 | 0.52 | 0.77 | 31 | ACT |
Interfaces
1 interface between chains.
- A–B · 4420 Ų buried · 62 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5G4I · PLP-dependent phospholyase A1RDF1 from Arthrobacter aurescens TC1 · 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 5G4I · PDBe 5G4I · UniProt A1RDF1
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