Research workbench
Crystal structure of the 1L-myo-inositol 1-phosphate synthase complexed with NADH
Analyse Crystal structure of the 1L-myo-inositol 1-phosphate synthase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1P1J
- Type
- protein
- Length
- 1,041 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inositol-3-phosphate synthase
- EC
- 5.5.1.4
- UniProt
- P11986
- Ligands
- NAI, PO4
- Pockets
- 15 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inositol-3-phosphate synthase (EC 5.5.1.4) | protein | 525 | 36% helix, 26% strand | P11986 |
| B | Inositol-3-phosphate synthase (EC 5.5.1.4) | protein | 516 | 37% helix, 26% strand | P11986 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 281 | 0.86 | 0.97 | 51 | PO4, NAI, GOL |
| 2 | 271 | 0.85 | 0.96 | 51 | PO4, NAI, GOL |
| 3 | 292 | 0.84 | 0.95 | 43 | empty |
| 4 | 195 | 0.57 | 0.80 | 28 | empty |
| 5 | 336 | 0.56 | 0.75 | 52 | empty |
Interfaces
1 interface between chains.
- A–B · 5988 Ų buried · 84 hydrogen bonds · protein-protein
Compared structures
- 1P1J · Crystal structure of the 1L-myo-inositol 1-phosphate synthase complexed with NADH · the same entry in another collection · chain A against A, TM-score 1.00
- P11986 · AlphaFold monomer V2.0 prediction for inositol-3-phosphate synthase (P11986) · 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 P11986
- Elsewhere: RCSB PDB 1P1J · PDBe 1P1J · UniProt P11986
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