Research workbench
Crystal structure of arabidopsis thaliana PDX1-I320 complex from multiple crystals
Analyse Crystal structure of arabidopsis thaliana PDX1-I320 complex from multiple… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LNV
- 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 0.68
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 | 47% helix, 13% strand | Q8L940 |
| B | Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6) | protein | 278 | 47% helix, 13% strand | Q8L940 |
| C | Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6) | protein | 276 | 46% helix, 14% strand | Q8L940 |
| D | Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6) | protein | 275 | 48% 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.68 | 0.94 | 25 | empty |
| 2 | 470 | 0.65 | 0.78 | 83 | SO4 |
| 3 | 215 | 0.60 | 0.81 | 27 | empty |
| 4 | 214 | 0.59 | 0.81 | 27 | empty |
| 5 | 380 | 0.59 | 0.76 | 40 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1098 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1071 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 959 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 941 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 443 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 5LNV · Crystal structure of Arabidopsis thaliana Pdx1-I320 complex from multiple crystals · 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 5LNV · PDBe 5LNV · UniProt Q8L940
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