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The crystal structure of L-idonate 5-dehydrogenase from escherichia COLI str. K-12 substr. MG1655
Analyse The crystal structure of L-idonate 5-dehydrogenase from escherichia COLI str.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DKH
- Type
- protein
- Length
- 1,382 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-idonate 5-dehydrogenase (NAD(P)(+))
- EC
- 1.1.1.264
- UniProt
- P39346
- Ligands
- ZN
- Pockets
- 19 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-idonate 5-dehydrogenase (NAD(P)(+)) (EC 1.1.1.264) | protein | 345 | 30% helix, 32% strand | P39346 |
| C, D | L-idonate 5-dehydrogenase (NAD(P)(+)) (EC 1.1.1.264) | protein | 346 | 27% helix, 32% strand | P39346 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 845 | 0.79 | 0.82 | 68 | empty |
| 2 | 933 | 0.77 | 0.80 | 75 | empty |
| 3 | 979 | 0.77 | 0.79 | 83 | empty |
| 4 | 879 | 0.77 | 0.80 | 80 | empty |
| 5 | 662 | 0.68 | 0.77 | 80 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1922 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 1849 Ų buried · 53 hydrogen bonds · protein-protein
- C–D · 582 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 581 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 67 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6DKH · The crystal structure of L-idonate 5-dehydrogenase from Escherichia coli str. K-12… · the same entry in another collection · chain A against A, TM-score 1.00
- P39346 · AlphaFold monomer V2.0 prediction for L-idonate 5-dehydrogenase (NAD(P)(+)) (P39346) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P39346
- Elsewhere: RCSB PDB 6DKH · PDBe 6DKH · UniProt P39346
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