MolNFT v1 · #11365 · protein
Myo-inositol-1-phosphate synthase complexed with an inhibitor, 2- deoxy-glucitol-6-phosphate
1JKI: “Myo-inositol-1-phosphate synthase complexed with an inhibitor, 2- deoxy-glucitol-6-phosphate”. X-ray diffraction, 3 ligands (DG6, NAI, NH4), 19 pockets (best druggability 0.87). MolNFT v1 #11365 on GenesisL1: 3D structure, binding…
- PDB
- 1JKI
- Type
- protein
- Length
- 1,049 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myo-inositol-1-phosphate synthase
- EC
- 5.5.1.4
- UniProt
- P11986
- Ligands
- DG6, NAI, NH4
- Pockets
- 19 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myo-inositol-1-phosphate synthase (EC 5.5.1.4) | protein | 525 | 35% helix, 26% strand | P11986 |
| B | Myo-inositol-1-phosphate synthase (EC 5.5.1.4) | protein | 524 | 33% helix, 24% strand | P11986 |
Ligands and binding sites
- DG6 · 2-deoxy-glucitol-6-phosphate · ligand · 2 copies · chains A, B
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
- NH4 · Ammonium ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 430 | 0.87 | 0.95 | 71 | NH4, DG6, NAI |
| 2 | 407 | 0.87 | 0.96 | 78 | NH4, DG6, NAI |
| 3 | 385 | 0.85 | 0.93 | 50 | empty |
| 4 | 57 | 0.68 | 0.96 | 23 | empty |
| 5 | 247 | 0.62 | 0.81 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 5950 Ų buried · 71 hydrogen bonds · protein-protein
Compared structures
- 1JKI · myo-Inositol-1-phosphate Synthase Complexed with an Inhibitor… · 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 A 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 1JKI · PDBe 1JKI · UniProt P11986
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