Research workbench
Crystal structure of pyridoxal biosynthesis lyase pdxs from pyrococcus
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
- 4FIR
- Type
- protein
- Length
- 1,998 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal biosynthesis lyase pdxs
- EC
- 4.-.-.-
- UniProt
- O59080
- Ligands
- R5P
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Pyridoxal biosynthesis lyase pdxs (EC 4.-.-.-) | protein | 333 | 49% helix, 13% strand | O59080 |
Ligands and binding sites
- R5P · Ribose-5-phosphate · 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.72 | 0.98 | 25 | R5P |
| 2 | 61 | 0.72 | 0.98 | 23 | R5P |
| 3 | 58 | 0.71 | 0.98 | 25 | R5P |
| 4 | 59 | 0.70 | 0.97 | 25 | R5P |
| 5 | 223 | 0.67 | 0.85 | 29 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1519 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 1502 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1492 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1488 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 1483 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent (covalent ligand).
Compared structures
- 4FIR · Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus · the same entry in another collection · chain C against C, 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 A 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 4FIR · PDBe 4FIR · UniProt O59080
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