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Crystal structure of phosphoesterase
Analyse Crystal structure of phosphoesterase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QAK
- Type
- protein
- Length
- 345 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2'-5'-RNA ligase
- EC
- 6.5.1.-
- UniProt
- P37025
- Ligands
- 2AM
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2'-5'-RNA ligase (EC 6.5.1.-) | protein | 171 | 27% helix, 36% strand | P37025 |
| B | 2'-5'-RNA ligase (EC 6.5.1.-) | protein | 174 | 28% helix, 38% strand | P37025 |
Ligands and binding sites
- 2AM · Adenosine-2'-monophosphate · ligand · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 603 | 0.80 | 0.85 | 51 | GOL, 2AM |
| 2 | 416 | 0.69 | 0.81 | 46 | empty |
Interfaces
1 interface between chains.
- A–B · 798 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
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 P37025
- Elsewhere: RCSB PDB 4QAK · PDBe 4QAK · UniProt P37025
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