Research workbench
Crystal structures of rat acid phosphatase complexed with the transitions state analogs vanadate and molybdate: implications for the reaction mechanism
Analyse Crystal structures of rat acid phosphatase complexed with the transitions state… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RPT
- Type
- protein
- Length
- 342 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prostatic acid phosphatase
- EC
- 3.1.3.2
- UniProt
- P20646
- Ligands
- NAG, BMA, VO4
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prostatic acid phosphatase (EC 3.1.3.2) | protein | 342 | 44% helix, 13% strand | P20646 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- VO4 · Vanadate 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 | 271 | 0.63 | 0.81 | 36 | VO4 |
| 2 | 94 | 0.44 | 0.79 | 19 | empty |
Modifications
Observed in the structure: 2 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1RPT · Crystal structures of rat acid phosphatase complexed with the transitions state analogs… · the same entry in another collection · chain A against A, TM-score 1.00
- P20646 · AlphaFold monomer V2.0 prediction for prostatic acid phosphatase (P20646) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P20646
- Elsewhere: RCSB PDB 1RPT · PDBe 1RPT · UniProt P20646
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