Research workbench
X-ray structure of the phosphatase PAPP5 from arabidopsis thaliana
Analyse X-ray structure of the phosphatase PAPP5 from arabidopsis thaliana in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OBE
- Type
- protein
- Length
- 955 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 2 of SERINE/THREONINE-protein phosphatase 5
- EC
- 3.1.3.16
- UniProt
- Q84XU2
- Ligands
- MN, CL
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform 2 of SERINE/THREONINE-protein phosphatase 5 (EC 3.1.3.16) | protein | 480 | 47% helix, 13% strand | Q84XU2 |
| B | Isoform 2 of SERINE/THREONINE-protein phosphatase 5 (EC 3.1.3.16) | protein | 475 | 48% helix, 12% strand | Q84XU2 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1037 | 0.82 | 0.83 | 107 | empty |
| 2 | 187 | 0.75 | 0.91 | 24 | empty |
| 3 | 240 | 0.68 | 0.84 | 21 | empty |
| 4 | 208 | 0.65 | 0.84 | 50 | CL |
| 5 | 94 | 0.58 | 0.86 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 755 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7OBE · X-ray structure of the phosphatase PAPP5 from Arabidopsis thaliana · the same entry in another collection · chain A against A, TM-score 1.00
- Q84XU2 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein phosphatase 5 (Q84XU2) · a predicted model of the same protein · chain B 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 Q84XU2
- Elsewhere: RCSB PDB 7OBE · PDBe 7OBE · UniProt Q84XU2
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