MolNFT v1 · #125931 · protein
Crystal structure of arabidopsis thaliana PDX1-I320 complex
5LNU · Pyridoxal 5'-phosphate synthase subunit PDX1.3: “Crystal structure of arabidopsis thaliana PDX1-I320 complex”. X-ray diffraction, 3 ligands (KIK, PO4, SO4), 8 pockets (best druggability 0.61). MolNFT v1 #125931 on GenesisL1: 3D…
- PDB
- 5LNU
- Type
- protein
- Length
- 1,106 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
- KIK, PO4, SO4
- Pockets
- 8 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6) | protein | 277 | 48% helix, 14% strand | Q8L940 |
| B | Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6) | protein | 278 | 46% helix, 14% strand | Q8L940 |
| C | 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 | 275 | 46% helix, 14% strand | Q8L940 |
Ligands and binding sites
- KIK · (4~{S})-4-azanyl-5-oxidanyl-pent-1-en-3-one · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
- SO4 · Sulfate 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
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 229 | 0.61 | 0.81 | 28 | empty |
| 2 | 216 | 0.59 | 0.81 | 28 | empty |
| 3 | 370 | 0.58 | 0.75 | 36 | empty |
| 4 | 182 | 0.52 | 0.78 | 37 | SO4 |
| 5 | 246 | 0.50 | 0.75 | 35 | SO4 |
Interfaces
5 interfaces between chains.
- A–B · 1097 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1084 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 961 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 950 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 450 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 5LNU · Crystal structure of Arabidopsis thaliana Pdx1-I320 complex · the same entry in another collection · chain D against D, 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 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 Q8L940
- Elsewhere: RCSB PDB 5LNU · PDBe 5LNU · UniProt Q8L940
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