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Structure of the hd-domain phosphohydrolase oxsa with oxetanocin-a diphosphate bound
Analyse Structure of the hd-domain phosphohydrolase oxsa with oxetanocin-a diphosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TK6
- Type
- protein
- Length
- 191 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxsa protein
- UniProt
- O24769
- Ligands
- 7D3, MG
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 69% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxsa protein | protein | 191 | 69% helix, 1% strand | O24769 |
Ligands and binding sites
- 7D3 · [(2S,3R,4R)-4-(6-amino-9H-purin-9-yl)-3-(hydroxymethyl)oxetan-2-yl]methyl trihydrogen diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.66 | 0.79 | 35 | MG, 7D3 |
| 2 | 133 | 0.43 | 0.75 | 19 | empty |
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 O24769
- Elsewhere: RCSB PDB 5TK6 · PDBe 5TK6 · UniProt O24769
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