Research workbench
Crystal structure of pyridoxal biosynthesis lyase pdxs from pyrococcus horikoshii
Analyse Crystal structure of pyridoxal biosynthesis lyase pdxs from pyrococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FIQ
- Type
- protein
- Length
- 1,920 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal biosynthesis lyase pdxs
- EC
- 4.-.-.-
- UniProt
- O59080
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 315 | 51% helix, 13% strand | O59080 |
| B, C, D, E, F | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 321 | 46% helix, 13% strand | O59080 |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 172 | 0.77 | 0.93 | 35 | empty |
| 2 | 113 | 0.76 | 0.96 | 28 | empty |
| 3 | 116 | 0.74 | 0.94 | 28 | empty |
| 4 | 170 | 0.74 | 0.91 | 31 | empty |
| 5 | 189 | 0.73 | 0.90 | 35 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1574 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1552 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1550 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 1523 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1501 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4FIQ · Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus horikoshii · the same entry in another collection · chain F against F, TM-score 1.00
- O59080 · AlphaFold monomer V2.0 prediction for pyridoxal 5'-phosphate synthase subunit pdxs… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 O59080
- Elsewhere: RCSB PDB 4FIQ · PDBe 4FIQ · UniProt O59080
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.