MolNFT v1 · #90020 · protein
Crystal structure of a probable sorbitol dehydrogenase (target psi- 012078) from sinorhizobium meliloti 1021
4E6P · Probable sorbitol dehydrogenase (L-iditol 2-dehydrogenase): “Crystal structure of a probable sorbitol dehydrogenase (target psi- 012078) from sinorhizobium meliloti 1021”. X-ray diffraction, 1 ligand (NA), 9 pockets (best…
- PDB
- 4E6P
- Type
- protein
- Length
- 1,024 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable sorbitol dehydrogenase (L-iditol 2-dehydrogenase)
- EC
- 1.1.1.14
- UniProt
- Q92N06
- Ligands
- NA
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Probable sorbitol dehydrogenase (L-iditol 2-dehydrogenase) (EC 1.1.1.14) | protein | 256 | 50% helix, 16% strand | Q92N06 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 693 | 0.87 | 0.91 | 47 | EDO |
| 2 | 1132 | 0.82 | 0.83 | 110 | EDO |
| 3 | 1069 | 0.82 | 0.83 | 105 | EDO |
| 4 | 92 | 0.36 | 0.75 | 17 | EDO |
| 5 | 76 | 0.34 | 0.75 | 18 | EDO |
Interfaces
6 interfaces between chains.
- A–B · 1584 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1581 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1562 Ų buried · 34 hydrogen bonds · protein-protein
- A–D · 1539 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 144 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 4E6P · Crystal structure of a probable sorbitol dehydrogenase (Target PSI-012078) from… · 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 Q92N06
- Elsewhere: RCSB PDB 4E6P · PDBe 4E6P · UniProt Q92N06
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