Research workbench
Crystal structure of PAAK2 in complex with phenylacetyl adenylate
Analyse Crystal structure of PAAK2 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
- 2Y4O
- Type
- protein
- Length
- 865 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
- B4EL89
- Ligands
- DLL, MG, K
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylacetate-coenzyme a ligase (EC 6.2.1.30) | protein | 433 | 35% helix, 25% strand | B4EL89 |
| B | Phenylacetate-coenzyme a ligase (EC 6.2.1.30) | protein | 432 | 35% helix, 26% strand | B4EL89 |
Ligands and binding sites
- DLL · 5'-O-[hydroxy(phenylacetyl)phosphoryl]adenosine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 674 | 0.83 | 0.87 | 99 | K, DLL |
| 2 | 545 | 0.81 | 0.87 | 90 | DLL, PEG, K |
| 3 | 190 | 0.48 | 0.75 | 18 | PEG |
| 4 | 59 | 0.45 | 0.84 | 16 | empty |
| 5 | 61 | 0.39 | 0.80 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 2013 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 2Y4O · Crystal Structure of PaaK2 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 B4EL89
- Elsewhere: RCSB PDB 2Y4O · PDBe 2Y4O · UniProt B4EL89
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