Research workbench
Structure of a mutant adenylate kinase ligated with an ATP-analogue showing domain closure over ATP
Analyse Structure of a mutant adenylate kinase ligated with an ATP-analogue showing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DVR
- Type
- protein
- Length
- 440 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate kinase
- EC
- 2.7.4.3
- UniProt
- P07170
- Ligands
- ATF
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenylate kinase (EC 2.7.4.3) | protein | 220 | 50% helix, 17% strand | P07170 |
Ligands and binding sites
- ATF · Phosphodifluoromethylphosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 545 | 0.77 | 0.84 | 62 | ATF |
| 2 | 433 | 0.74 | 0.84 | 45 | ATF |
| 3 | 455 | 0.73 | 0.82 | 55 | empty |
Interfaces
1 interface between chains.
- A–B · 1323 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1DVR · Structure of a mutant adenylate kinase ligated with an ATP-analogue showing domain… · the same entry in another collection · chain A against A, TM-score 1.00
- P07170 · AlphaFold monomer V2.0 prediction for adenylate kinase (P07170) · a predicted model of the same protein · chain A against A, TM-score 0.83
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 P07170
- Elsewhere: RCSB PDB 1DVR · PDBe 1DVR · UniProt P07170
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