Research workbench
Plps (inactive glutaminase mutant) co-crystallized with glutamine and R5P.
Analyse Plps (inactive glutaminase mutant) co-crystallized with glutamine and R5P. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WXY
- Type
- protein
- Length
- 2,875 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal biosynthesis lyase pdxs; Glutamine amidotransferase subunit pdxt
- EC
- 4.-.-.-, 2.6.-.-
- UniProt
- Q5L3Y2, Q5L3Y1
- Ligands
- L5P
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 8 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, I | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 287 | 46% helix, 12% strand | Q5L3Y2 |
| C, G, K | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 289 | 46% helix, 12% strand | Q5L3Y2 |
| E | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 288 | 46% helix, 13% strand | Q5L3Y2 |
| B | Glutamine amidotransferase subunit pdxt (EC 2.6.-.-) | protein | 188 | 30% helix, 32% strand | Q5L3Y1 |
| D, H | Glutamine amidotransferase subunit pdxt (EC 2.6.-.-) | protein | 192 | 31% helix, 34% strand | Q5L3Y1 |
| F | Glutamine amidotransferase subunit pdxt (EC 2.6.-.-) | protein | 194 | 31% helix, 34% strand | Q5L3Y1 |
| J | Glutamine amidotransferase subunit pdxt (EC 2.6.-.-) | protein | 189 | 30% helix, 35% strand | Q5L3Y1 |
| L | Glutamine amidotransferase subunit pdxt (EC 2.6.-.-) | protein | 191 | 31% helix, 32% strand | Q5L3Y1 |
Ligands and binding sites
- L5P · (2S)-2-azanyl-6-[[(3R,4R)-3,4-bis(oxidanyl)-2-oxidanylidene-5-phosphonooxy-pentyl]amino]hexanoic acid · ligand · 6 copies · chains A, C, E, G, I, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.80 | 0.97 | 38 | L5P |
| 2 | 309 | 0.78 | 0.89 | 57 | L5P |
| 3 | 318 | 0.78 | 0.89 | 56 | L5P |
| 4 | 304 | 0.78 | 0.89 | 57 | L5P |
| 5 | 148 | 0.78 | 0.95 | 40 | L5P |
Interfaces
19 interfaces between chains.
- C–D · 1748 Ų buried · 36 hydrogen bonds · protein-protein
- K–L · 1738 Ų buried · 36 hydrogen bonds · protein-protein
- G–H · 1738 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 1723 Ų buried · 37 hydrogen bonds · protein-protein
- I–J · 1693 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent, 6 modified (covalent ligand, nonstandard).
Compared structures
- 4WXY · PLPS (inactive glutaminase mutant) co-crystallized with glutamine and R5P. · the same entry in another collection · chain L against L, 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 Q5L3Y2
- Every structure of UniProt Q5L3Y1
- Elsewhere: RCSB PDB 4WXY · PDBe 4WXY · UniProt Q5L3Y2 · UniProt Q5L3Y1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.