Research workbench
Crystal structure of yeast YMX7, an ADP-ribose-1''-monophosphatase, complexed with ADP
Analyse Crystal structure of yeast YMX7, an ADP-ribose-1''-monophosphatase, complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TY8
- Type
- protein
- Length
- 249 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical 32.1 kda protein in ADH3-RCA1 intergenic region
- UniProt
- Q04299
- Ligands
- ADP, NA, CL
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical 32.1 kda protein in ADH3-RCA1 intergenic region | protein | 249 | 44% helix, 15% strand | Q04299 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · 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 | 176 | 0.59 | 0.82 | 33 | NA, CL, ADP |
| 2 | 50 | 0.30 | 0.76 | 15 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1TY8 · Crystal structure of yeast ymx7, an ADP-ribose-1''-monophosphatase, complexed with ADP · the same entry in another collection · chain A against A, TM-score 1.00
- Q04299 · AlphaFold monomer V2.0 prediction for probable ADP-ribose 1''-phosphate phosphatase… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q04299
- Elsewhere: RCSB PDB 1TY8 · PDBe 1TY8 · UniProt Q04299
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