MolNFT v1 · #20672 · protein
Crystal structure of myo-inositol 1-phosphate synthase from saccharomyces cerevisiae in complex with NAD+ and 2-deoxy-D-glucitol 6-(E)-vinylhomophosphonate
1RM0 · Myo-inositol-phosphate synthase: “Crystal structure of myo-inositol 1-phosphate synthase from saccharomyces cerevisiae in complex with NAD+ and…”. X-ray diffraction, 3 ligands (NAI, D6P, MN), 17 pockets (best druggability 0.85).…
- PDB
- 1RM0
- Type
- protein
- Length
- 1,041 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myo-inositol-phosphate synthase
- EC
- 5.5.1.4
- Ligands
- NAI, D6P, MN
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myo-inositol-phosphate synthase (EC 5.5.1.4) | protein | 525 | 35% helix, 26% strand | — |
| B | Myo-inositol-phosphate synthase (EC 5.5.1.4) | protein | 516 | 37% helix, 27% strand | — |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
- D6P · (3,4,5,7-tetrahydroxy-hept-1-enyl)-phosphonic acid · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.85 | 0.97 | 51 | MN, D6P, NAI |
| 2 | 335 | 0.84 | 0.94 | 45 | empty |
| 3 | 352 | 0.84 | 0.93 | 71 | NAI |
| 4 | 191 | 0.58 | 0.81 | 30 | empty |
| 5 | 96 | 0.51 | 0.83 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 5972 Ų buried · 85 hydrogen bonds · protein-protein
Compared structures
- 1RM0 · Crystal Structure of Myo-Inositol 1-Phosphate Synthase From Saccharomyces cerevisiae In… · 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
- Elsewhere: RCSB PDB 1RM0 · PDBe 1RM0
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