Research workbench
2.4 ångström resolution crystal structure of putative sugar kinase from campylobacter jejuni.
Analyse 2.4 ångström resolution crystal structure of putative sugar kinase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N3O
- Type
- protein
- Length
- 642 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative D-glycero-D-manno-heptose 7-phosphate kinase
- UniProt
- Q0P8I9
- Ligands
- CA
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative D-glycero-D-manno-heptose 7-phosphate kinase | protein | 328 | 38% helix, 29% strand | Q0P8I9 |
| B | Putative D-glycero-D-manno-heptose 7-phosphate kinase | protein | 314 | 37% helix, 29% strand | Q0P8I9 |
Ligands and binding sites
- CA · Calcium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 785 | 0.82 | 0.85 | 98 | empty |
| 2 | 214 | 0.54 | 0.78 | 37 | empty |
| 3 | 120 | 0.50 | 0.80 | 23 | empty |
| 4 | 142 | 0.49 | 0.79 | 25 | empty |
| 5 | 50 | 0.37 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1481 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 4N3O · 2.4 Angstrom Resolution Crystal Structure of Putative Sugar Kinase from Campylobacter… · 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 Q0P8I9
- Elsewhere: RCSB PDB 4N3O · PDBe 4N3O · UniProt Q0P8I9
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