Research workbench
Crystal structure of had-like phosphatase yida from E. COLI
Analyse Crystal structure of had-like phosphatase yida from E. COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RKQ
- Type
- protein
- Length
- 542 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein yida
- UniProt
- P0A8Y5
- Ligands
- MG, CL
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hypothetical protein yida | protein | 271 | 41% helix, 23% strand | P0A8Y5 |
Ligands and binding sites
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 | 753 | 0.70 | 0.77 | 68 | empty |
| 2 | 139 | 0.59 | 0.84 | 33 | CL, MG |
| 3 | 147 | 0.56 | 0.82 | 29 | CL, MG |
Interfaces
1 interface between chains.
- A–B · 277 Ų buried · 5 hydrogen bonds · protein-protein
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 P0A8Y5
- Elsewhere: RCSB PDB 1RKQ · PDBe 1RKQ · UniProt P0A8Y5
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