Research workbench
Structural analysis of saccharomyces cerevisiae myo-inositol phosphate synthase
Analyse Structural analysis of saccharomyces cerevisiae myo-inositol phosphate synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LA2
- Type
- protein
- Length
- 2,056 residues
- Chains
- 4
- 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
- NAD
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Myo-inositol-1-phosphate synthase (EC 5.5.1.4) | protein | 514 | 31% helix, 26% strand | P11986 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 679 | 0.85 | 0.89 | 89 | empty |
| 2 | 535 | 0.84 | 0.90 | 68 | empty |
| 3 | 600 | 0.83 | 0.88 | 84 | NAD |
| 4 | 821 | 0.83 | 0.85 | 95 | empty |
| 5 | 823 | 0.82 | 0.85 | 86 | empty |
Interfaces
6 interfaces between chains.
- C–D · 6046 Ų buried · 78 hydrogen bonds · protein-protein
- A–B · 5999 Ų buried · 79 hydrogen bonds · protein-protein
- B–C · 997 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 986 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 598 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified (engineered).
Compared structures
- 1LA2 · Structural analysis of Saccharomyces cerevisiae myo-inositol phosphate synthase · 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 1LA2 · PDBe 1LA2 · UniProt P11986
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