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Crystal structure of a sugar kinase (target efi-502312) from oceanicola granulosus, with bound AMP/ADP crystal form I
Analyse Crystal structure of a sugar kinase (target efi-502312) from oceanicola… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EBU
- Type
- protein
- Length
- 306 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-dehydro-3-deoxygluconokinase
- EC
- 2.7.1.45
- UniProt
- Q2CIP5
- Ligands
- ADP, CL
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-dehydro-3-deoxygluconokinase (EC 2.7.1.45) | protein | 306 | 39% helix, 22% strand | Q2CIP5 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 466 | 0.67 | 0.78 | 51 | ADP |
| 2 | 114 | 0.38 | 0.74 | 24 | empty |
Compared structures
- 4EBU · Crystal structure of a sugar kinase (Target EFI-502312) from Oceanicola granulosus, with… · 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 4EBU · PDBe 4EBU · UniProt Q2CIP5
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