MolNFT v1 · #125929 · protein
Crystal structure of arabidopsis thaliana PDX1-R5P complex
5LNS · Pyridoxal 5'-phosphate synthase subunit PDX1.3: “Crystal structure of arabidopsis thaliana PDX1-R5P complex”. X-ray diffraction, 2 ligands (5RP, PO4), 12 pockets (best druggability 0.72). MolNFT v1 #125929 on GenesisL1: 3D…
- PDB
- 5LNS
- Type
- protein
- Length
- 1,099 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
- 5RP, PO4
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 47% 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 | 275 | 48% helix, 14% strand | Q8L940 |
| B | Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6) | protein | 276 | 47% helix, 14% strand | Q8L940 |
| D | Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6) | protein | 273 | 48% helix, 15% strand | Q8L940 |
Ligands and binding sites
- 5RP · Ribulose-5-phosphate · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.72 | 0.98 | 24 | 5RP |
| 2 | 60 | 0.72 | 0.98 | 24 | 5RP |
| 3 | 57 | 0.71 | 0.98 | 25 | 5RP |
| 4 | 65 | 0.70 | 0.97 | 25 | 5RP |
| 5 | 83 | 0.70 | 0.94 | 25 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1080 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1059 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 969 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 953 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 474 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5LNS · Crystal structure of Arabidopsis thaliana Pdx1-R5P 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 D against A, 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 Q8L940
- Elsewhere: RCSB PDB 5LNS · PDBe 5LNS · UniProt Q8L940
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