Research workbench
Crystal structure of nucleoside kinase from chlorobium tepidum in complex with AMP
Analyse Crystal structure of nucleoside kinase from chlorobium tepidum in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KD6
- Type
- protein
- Length
- 598 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbohydrate kinase, pfkb family
- UniProt
- Q8KDR9
- Ligands
- AMP
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbohydrate kinase, pfkb family | protein | 300 | 38% helix, 26% strand | Q8KDR9 |
| B | Carbohydrate kinase, pfkb family | protein | 298 | 38% helix, 25% strand | Q8KDR9 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.80 | 0.90 | 44 | AMP, GOL |
| 2 | 334 | 0.80 | 0.90 | 45 | AMP, GOL |
| 3 | 273 | 0.57 | 0.78 | 35 | empty |
| 4 | 255 | 0.57 | 0.78 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 515 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3KD6 · Crystal Structure of Nucleoside Kinase from Chlorobium tepidum in Complex with AMP · 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 Q8KDR9
- Elsewhere: RCSB PDB 3KD6 · PDBe 3KD6 · UniProt Q8KDR9
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