MolNFT v1 · #112071 · protein
Crystal structure of 2-keto-3-deoxy-D-gluconate dehydrogenase from pectobacterium carotovorum
4Z9Y · 2-deoxy-D-gluconate 3-dehydrogenase: “Crystal structure of 2-keto-3-deoxy-D-gluconate dehydrogenase from pectobacterium carotovorum”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.86). MolNFT v1 #112071 on…
- PDB
- 4Z9Y
- Type
- protein
- Length
- 1,012 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-deoxy-D-gluconate 3-dehydrogenase
- EC
- 1.1.1.127
- UniProt
- A0A093RP61
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 2-deoxy-D-gluconate 3-dehydrogenase (EC 1.1.1.127) | protein | 253 | 51% helix, 16% strand | A0A093RP61 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 760 | 0.86 | 0.89 | 57 | empty |
| 2 | 1180 | 0.83 | 0.84 | 107 | SO4 |
| 3 | 616 | 0.76 | 0.82 | 55 | SO4 |
| 4 | 760 | 0.76 | 0.81 | 69 | SO4 |
| 5 | 51 | 0.46 | 0.85 | 12 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1858 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1811 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1512 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 1509 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 378 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4Z9Y · Crystal structure of 2-keto-3-deoxy-D-gluconate dehydrogenase from Pectobacterium… · 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 A0A093RP61
- Elsewhere: RCSB PDB 4Z9Y · PDBe 4Z9Y · UniProt A0A093RP61
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.