Research workbench
PAAK1 in complex with phenylacetyl adenylate
Analyse PAAK1 in complex with phenylacetyl adenylate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y4N
- Type
- protein
- Length
- 849 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylacetate-coenzyme a ligase
- EC
- 6.2.1.30
- UniProt
- B4E7B5
- Ligands
- DLL, PAC, MG
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylacetate-coenzyme a ligase (EC 6.2.1.30) | protein | 426 | 35% helix, 24% strand | B4E7B5 |
| B | Phenylacetate-coenzyme a ligase (EC 6.2.1.30) | protein | 423 | 35% helix, 24% strand | B4E7B5 |
Ligands and binding sites
- DLL · 5'-O-[hydroxy(phenylacetyl)phosphoryl]adenosine · ligand · 2 copies · chains A, B
- PAC · 2-phenylacetic acid · ligand · chains B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
- PGE · Triethylene glycol · additive · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1125 | 0.79 | 0.81 | 130 | DLL, PAC, BME |
| 2 | 186 | 0.49 | 0.76 | 30 | MG, BME |
| 3 | 165 | 0.46 | 0.75 | 31 | MG, BME |
| 4 | 113 | 0.38 | 0.74 | 16 | empty |
| 5 | 52 | 0.26 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1593 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 2Y4N · PaaK1 in complex with phenylacetyl adenylate · 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 B4E7B5
- Elsewhere: RCSB PDB 2Y4N · PDBe 2Y4N · UniProt B4E7B5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.