Research workbench
Pdxs (G. stearothermophilus) co-crystallized with R5P in the presence of ammonia.
Analyse Pdxs (G. stearothermophilus) co-crystallized with R5P in the presence of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WY0
- Type
- protein
- Length
- 2,980 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal biosynthesis lyase pdxs
- EC
- 4.-.-.-
- UniProt
- Q5L3Y2
- Ligands
- L5P, R5P, PO4
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 10 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, K | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 247 | 48% helix, 14% strand | Q5L3Y2 |
| B | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 260 | 49% helix, 15% strand | Q5L3Y2 |
| C, E | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 246 | 47% helix, 15% strand | Q5L3Y2 |
| D | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 247 | 48% helix, 16% strand | Q5L3Y2 |
| F | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 248 | 48% helix, 15% strand | Q5L3Y2 |
| G | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 256 | 50% helix, 14% strand | Q5L3Y2 |
| H | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 246 | 48% helix, 16% strand | Q5L3Y2 |
| I | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 248 | 48% helix, 15% strand | Q5L3Y2 |
| J | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 244 | 49% helix, 15% strand | Q5L3Y2 |
| L | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 245 | 49% helix, 15% strand | Q5L3Y2 |
Ligands and binding sites
- L5P · (2S)-2-azanyl-6-[[(3R,4R)-3,4-bis(oxidanyl)-2-oxidanylidene-5-phosphonooxy-pentyl]amino]hexanoic acid · ligand · 8 copies · chains A, C, E, G, I, J, K, L
- R5P · Ribose-5-phosphate · ligand · 7 copies · chains B, J, D, L, E, I, A, G, F, K
- PO4 · Phosphate ion · ion · 4 copies · chains B, D, F, H
- CAC · Cacodylate ion · additive · 5 copies · chains A, G, C, H, F, K, D, L
- EDO · 1,2-ethanediol · additive · 3 copies · chains C, H, K, G, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.70 | 0.81 | 51 | L5P |
| 2 | 489 | 0.69 | 0.80 | 55 | L5P |
| 3 | 462 | 0.69 | 0.80 | 55 | L5P |
| 4 | 449 | 0.68 | 0.80 | 57 | L5P |
| 5 | 440 | 0.64 | 0.78 | 58 | R5P |
Interfaces
24 interfaces between chains.
- B–G · 973 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 972 Ų buried · 12 hydrogen bonds · protein-protein
- C–K · 968 Ų buried · 10 hydrogen bonds · protein-protein
- F–H · 957 Ų buried · 10 hydrogen bonds · protein-protein
- A–J · 950 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 4WY0 · PdxS (G. stearothermophilus) co-crystallized with R5P in the presence of ammonia. · the same entry in another collection · chain K against K, 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
- Elsewhere: RCSB PDB 4WY0 · PDBe 4WY0 · UniProt Q5L3Y2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.