Research workbench
Crystal structure of arabidopsis thaliana PDX1K166R-PREI320 complex
Analyse Crystal structure of arabidopsis thaliana PDX1K166R-PREI320 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LNT
- Type
- protein
- Length
- 1,088 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal 5'-phosphate synthase subunit PDX1.1
- EC
- 4.3.3.6
- UniProt
- O80448
- Ligands
- KPR, PO4
- Pockets
- 14 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxal 5'-phosphate synthase subunit PDX1.1 (EC 4.3.3.6) | protein | 273 | 47% helix, 14% strand | O80448 |
| B, C | Pyridoxal 5'-phosphate synthase subunit PDX1.1 (EC 4.3.3.6) | protein | 272 | 47% helix, 14% strand | O80448 |
| D | Pyridoxal 5'-phosphate synthase subunit PDX1.1 (EC 4.3.3.6) | protein | 271 | 46% helix, 14% strand | O80448 |
Ligands and binding sites
- KPR · [(~{E},4~{S})-4-azanyl-3-oxidanylidene-pent-1-enyl] dihydrogen 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
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.66 | 0.95 | 27 | empty |
| 2 | 103 | 0.63 | 0.89 | 27 | KPR |
| 3 | 104 | 0.63 | 0.88 | 29 | KPR |
| 4 | 128 | 0.61 | 0.86 | 30 | KPR |
| 5 | 198 | 0.60 | 0.82 | 25 | empty |
Interfaces
5 interfaces between chains.
- B–C · 933 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 926 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 920 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 912 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 407 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5LNT · Crystal structure of Arabidopsis thaliana Pdx1K166R-preI320 complex · the same entry in another collection · chain A against A, TM-score 1.00
- O80448 · AlphaFold monomer V2.0 prediction for pyridoxal 5'-phosphate synthase subunit PDX1.1… · a predicted model of the same protein · chain B 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 O80448
- Elsewhere: RCSB PDB 5LNT · PDBe 5LNT · UniProt O80448
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