Research workbench
Crystal structure of human adenylate kinase 4 (AK4) in complex with diguanosine pentaphosphate
Analyse Crystal structure of human adenylate kinase 4 (AK4) in complex with diguanosine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BBW
- Type
- protein
- Length
- 440 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate kinase 4, AK4
- EC
- 2.7.4.3
- UniProt
- P27144
- Ligands
- GP5
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenylate kinase 4, AK4 (EC 2.7.4.3) | protein | 220 | 48% helix, 15% strand | P27144 |
Ligands and binding sites
- GP5 · Diguanosine-pentaphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 822 | 0.72 | 0.78 | 62 | GP5 |
| 2 | 659 | 0.69 | 0.77 | 56 | GP5 |
| 3 | 395 | 0.58 | 0.75 | 31 | empty |
| 4 | 54 | 0.33 | 0.77 | 12 | empty |
| 5 | 51 | 0.28 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 174 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2BBW · Crystal structure of human adenylate kinase 4 (AK4) in complex with diguanosine… · the same entry in another collection · chain A against A, TM-score 1.00
- P27144 · AlphaFold monomer V2.0 prediction for adenylate kinase 4, mitochondrial (P27144) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P27144
- Elsewhere: RCSB PDB 2BBW · PDBe 2BBW · UniProt P27144
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