Research workbench
Catalytic domain of human SERINE/THREONINE phosphatase 5 (PP5C) with two MN2+ atoms originally soaked with cantharidin (which is present in the structure in the hydrolyzed form)
Analyse Catalytic domain of human SERINE/THREONINE phosphatase 5 (PP5C) with two MN2+… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H63
- Type
- protein
- Length
- 630 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein phosphatase 5
- EC
- 3.1.3.16
- UniProt
- P53041
- Ligands
- NHC, MN
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | SERINE/THREONINE-protein phosphatase 5 (EC 3.1.3.16) | protein | 315 | 35% helix, 20% strand | P53041 |
Ligands and binding sites
- NHC · (1R,2S,3R,4S)-2,3-dimethyl-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid · ligand · 2 copies · chains A, C
- MN · Manganese (II) ion · metal · 4 copies · chains A, C
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 | 556 | 0.62 | 0.74 | 50 | MN, NHC |
| 2 | 75 | 0.36 | 0.76 | 17 | MN, NHC |
Interfaces
1 interface between chains.
- A–C · 195 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3H63 · Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c) with two Mn2+ atoms… · the same entry in another collection · chain A against A, TM-score 1.00
- P53041 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein phosphatase 5 (P53041) · a predicted model of the same protein · 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 P53041
- Elsewhere: RCSB PDB 3H63 · PDBe 3H63 · UniProt P53041
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