Research workbench
Crystal structure of notothenia coriiceps adenylate kinase variant
Analyse Crystal structure of notothenia coriiceps adenylate kinase variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XRU
- Type
- protein
- Length
- 372 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate kinase
- Ligands
- AP5, SO4
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 59% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenylate kinase | protein | 186 | 59% helix, 15% strand | — |
Ligands and binding sites
- AP5 · Bis(adenosine)-5'-pentaphosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 309 | 0.75 | 0.87 | 37 | AP5 |
| 2 | 321 | 0.74 | 0.86 | 47 | AP5 |
| 3 | 131 | 0.39 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 310 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5XRU · Crystal structure of Notothenia coriiceps adenylate kinase variant · 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
- Elsewhere: RCSB PDB 5XRU · PDBe 5XRU
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