Research workbench
Crystal structure of myo-inositol 2-dehydrogenase (NP_786804.1) from lactobacillus plantarum at 2.40 a resolution
Analyse Crystal structure of myo-inositol 2-dehydrogenase (NP_786804.1) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CEA
- Type
- protein
- Length
- 1,362 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myo-inositol 2-dehydrogenase
- EC
- 1.1.1.18
- UniProt
- Q88S39
- Ligands
- NAD, CL
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Myo-inositol 2-dehydrogenase (EC 1.1.1.18) | protein | 342 | 41% helix, 26% strand | Q88S39 |
| C, D | Myo-inositol 2-dehydrogenase (EC 1.1.1.18) | protein | 339 | 43% helix, 27% strand | Q88S39 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 3 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1021 | 0.84 | 0.86 | 93 | EDO |
| 2 | 538 | 0.76 | 0.83 | 59 | NAD |
| 3 | 431 | 0.75 | 0.84 | 43 | NAD |
| 4 | 396 | 0.75 | 0.85 | 43 | NAD |
| 5 | 520 | 0.75 | 0.83 | 54 | NAD |
Interfaces
6 interfaces between chains.
- B–C · 1747 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1733 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1216 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 1208 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 651 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified (engineered).
Compared structures
- 3CEA · Crystal structure of myo-inositol 2-dehydrogenase (NP_786804.1) from Lactobacillus… · 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 Q88S39
- Elsewhere: RCSB PDB 3CEA · PDBe 3CEA · UniProt Q88S39
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