MolNFT v1 · #90008 · protein
Crystal structure of a sugar kinase (target efi-502132) from oceanicola granulosus, unliganded structure
4E69 · 2-dehydro-3-deoxygluconokinase: “Crystal structure of a sugar kinase (target efi-502132) from oceanicola granulosus, unliganded structure”. X-ray diffraction, 1 ligand (CL), 4 pockets (best druggability 0.69). MolNFT v1 #90008 on…
- PDB
- 4E69
- Type
- protein
- Length
- 621 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-dehydro-3-deoxygluconokinase
- UniProt
- Q2CIP5
- Ligands
- CL
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-dehydro-3-deoxygluconokinase | protein | 310 | 38% helix, 24% strand | Q2CIP5 |
| B | 2-dehydro-3-deoxygluconokinase | protein | 311 | 38% helix, 24% strand | Q2CIP5 |
Ligands and binding sites
- CL · Chloride ion · ion · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 562 | 0.69 | 0.78 | 66 | CL, GOL |
| 2 | 501 | 0.69 | 0.79 | 50 | CL, EDO |
| 3 | 304 | 0.58 | 0.78 | 41 | empty |
| 4 | 166 | 0.46 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 950 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4E69 · Crystal structure of a sugar kinase (target EFI-502132) from Oceanicola granulosus… · 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 Q2CIP5
- Elsewhere: RCSB PDB 4E69 · PDBe 4E69 · UniProt Q2CIP5
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