MolNFT v1 · #25273 · protein
Crystal structure of inositol-3-phosphate synthase (CE21227) from caenorhabditis elegans at 2.30 a resolution
1VKO: “Crystal structure of inositol-3-phosphate synthase (CE21227) from caenorhabditis elegans at 2.30 a resolution”. X-ray diffraction, 5 ligands (NAD, POP, K), 7 pockets (best druggability 0.84). MolNFT v1 #25273 on GenesisL1: 3D…
- PDB
- 1VKO
- Type
- protein
- Length
- 511 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inositol-3-phosphate synthase
- EC
- 5.5.1.4
- UniProt
- Q18664
- Ligands
- NAD, POP, K, CL, IOD
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inositol-3-phosphate synthase (EC 5.5.1.4) | protein | 511 | 36% helix, 26% strand | Q18664 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- POP · Pyrophosphate 2- · ligand · chains A
- K · Potassium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- IOD · Iodide ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.84 | 0.96 | 50 | K, NAD, POP |
| 2 | 360 | 0.59 | 0.76 | 28 | empty |
| 3 | 136 | 0.52 | 0.80 | 19 | empty |
| 4 | 100 | 0.39 | 0.76 | 16 | CL |
| 5 | 145 | 0.39 | 0.73 | 23 | empty |
Compared structures
- 1VKO · Crystal structure of inositol-3-phosphate synthase (ce21227) from Caenorhabditis elegans… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q18664
- Elsewhere: RCSB PDB 1VKO · PDBe 1VKO · UniProt Q18664
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