Research workbench
Crystal structure of apha class B acid PHOSPHATASE/PHOSPHOTRANSFERASE ternary complex with deoxycytosine and phosphate bound to the catalytic metal
Analyse Crystal structure of apha class B acid PHOSPHATASE/PHOSPHOTRANSFERASE ternary… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RMY
- Type
- protein
- Length
- 418 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Class B acid phosphatase
- EC
- 3.1.3.2
- UniProt
- P32697
- Ligands
- DCZ, MG, PO4
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Class B acid phosphatase (EC 3.1.3.2) | protein | 209 | 36% helix, 16% strand | P32697 |
Ligands and binding sites
- DCZ · 2'-deoxycytidine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 379 | 0.68 | 0.81 | 47 | PO4, DCZ |
| 2 | 222 | 0.57 | 0.79 | 28 | DCZ |
| 3 | 56 | 0.40 | 0.81 | 14 | empty |
| 4 | 81 | 0.35 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1376 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1RMY · Crystal structure of AphA class B acid phosphatase/phosphotransferase ternary complex… · 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 P32697
- Elsewhere: RCSB PDB 1RMY · PDBe 1RMY · UniProt P32697
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