MolNFT v1 · #125928 · protein
Crystal structure of arabidopsis thaliana PDX1-plp complex
5LNR · Pyridoxal 5'-phosphate synthase subunit PDX1.3: “Crystal structure of arabidopsis thaliana PDX1-plp complex”. X-ray diffraction, 1 ligand (PLP), 10 pockets (best druggability 0.65). MolNFT v1 #125928 on GenesisL1: 3D structure…
- PDB
- 5LNR
- Type
- protein
- Length
- 1,066 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal 5'-phosphate synthase subunit PDX1.3
- EC
- 4.3.3.6
- UniProt
- Q8L940
- Ligands
- PLP
- Pockets
- 10 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6) | protein | 267 | 51% helix, 14% strand | Q8L940 |
| B, D | Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6) | protein | 266 | 49% helix, 14% strand | Q8L940 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, D, B, C
- GOL · Glycerol · additive · 8 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.65 | 0.82 | 37 | GOL |
| 2 | 258 | 0.64 | 0.82 | 34 | GOL |
| 3 | 256 | 0.64 | 0.82 | 34 | GOL |
| 4 | 297 | 0.63 | 0.80 | 41 | GOL |
| 5 | 344 | 0.57 | 0.76 | 40 | empty |
Interfaces
5 interfaces between chains.
- A–D · 997 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 979 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 956 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 954 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 478 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5LNR · Crystal structure of Arabidopsis thaliana Pdx1-PLP complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q8L940 · AlphaFold monomer V2.0 prediction for pyridoxal 5'-phosphate synthase subunit PDX1.3… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q8L940
- Elsewhere: RCSB PDB 5LNR · PDBe 5LNR · UniProt Q8L940
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