MolNFT v1 · #109279 · protein
Pdxs (G. stearothermophilus) co-crystallized with R5P
4WXZ · Pyridoxal biosynthesis lyase pdxs: “Pdxs (G. stearothermophilus) co-crystallized with R5P”. X-ray diffraction, 1 ligand (L5P), 20 pockets (best druggability 0.70). MolNFT v1 #109279 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4WXZ
- Type
- protein
- Length
- 1,468 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal biosynthesis lyase pdxs
- EC
- 4.-.-.-
- UniProt
- Q5L3Y2
- Ligands
- L5P
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 6 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 243 | 47% helix, 13% strand | Q5L3Y2 |
| B | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 242 | 47% helix, 13% strand | Q5L3Y2 |
| C | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 255 | 48% helix, 12% strand | Q5L3Y2 |
| D | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 244 | 46% helix, 14% strand | Q5L3Y2 |
| E | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 241 | 47% helix, 13% strand | Q5L3Y2 |
| F | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 243 | 47% helix, 13% 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 · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.70 | 0.80 | 59 | L5P |
| 2 | 317 | 0.68 | 0.82 | 39 | L5P |
| 3 | 298 | 0.65 | 0.81 | 38 | L5P |
| 4 | 262 | 0.65 | 0.82 | 36 | L5P |
| 5 | 284 | 0.65 | 0.81 | 38 | L5P |
Interfaces
9 interfaces between chains.
- A–B · 972 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 971 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 966 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 958 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 906 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent, 6 modified (covalent ligand, nonstandard).
Compared structures
- 4WXZ · PdxS (G. stearothermophilus) co-crystallized with R5P · the same entry in another collection · chain F against F, TM-score 1.00
- Q5L3Y2 · AlphaFold monomer V2.0 prediction for pyridoxal 5'-phosphate synthase subunit pdxs… · a predicted model of the same protein · chain C against A, TM-score 0.99
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 4WXZ · PDBe 4WXZ · UniProt Q5L3Y2
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