Research workbench
Structure of adenylate kinase 1 in complex with P1,P4-DI(ADENOSINE) tetraphosphate
Analyse Structure of adenylate kinase 1 in complex with P1,P4-DI(ADENOSINE)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C95
- Type
- protein
- Length
- 389 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate kinase 1
- EC
- 2.7.4.3
- UniProt
- P00568
- Ligands
- B4P
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylate kinase 1 (EC 2.7.4.3) | protein | 195 | 61% helix, 13% strand | P00568 |
| B | Adenylate kinase 1 (EC 2.7.4.3) | protein | 194 | 59% helix, 13% strand | P00568 |
Ligands and binding sites
- B4P · Bis(adenosine)-5'-tetraphosphate · ligand · 2 copies · chains A, B
- MLI · Malonate ion · additive · 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 | 327 | 0.76 | 0.87 | 50 | B4P |
| 2 | 293 | 0.75 | 0.88 | 43 | B4P |
| 3 | 311 | 0.58 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 326 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2C95 · Structure of adenylate kinase 1 in complex with P1,P4-di(adenosine) tetraphosphate · the same entry in another collection · chain A against A, TM-score 1.00
- P00568 · AlphaFold monomer V2.0 prediction for adenylate kinase isoenzyme 1 (P00568) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P00568
- Elsewhere: RCSB PDB 2C95 · PDBe 2C95 · UniProt P00568
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