MolNFT v1 · #124005 · protein
Crystal structure of human phosphatase prl-2 in complex with the ADP- bound bateman domain of human magnesium transporter CNNM3
5K25 · Protein tyrosine phosphatase type iva 2: “Crystal structure of human phosphatase prl-2 in complex with the ADP- bound bateman domain of human magnesium…”. X-ray diffraction, 1 ligand (ADP), 2 pockets (best druggability 0.68). MolNFT…
- PDB
- 5K25
- Type
- protein
- Length
- 307 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein tyrosine phosphatase type iva 2; Metal transporter CNNM3
- EC
- 3.1.3.48
- UniProt
- Q12974, Q8NE01
- Ligands
- ADP
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein tyrosine phosphatase type iva 2 (EC 3.1.3.48) | protein | 157 | 41% helix, 18% strand | Q12974 |
| C | Metal transporter CNNM3 | protein | 150 | 35% helix, 23% strand | Q8NE01 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains 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 | 643 | 0.68 | 0.77 | 48 | empty |
| 2 | 72 | 0.35 | 0.77 | 16 | ADP |
Interfaces
1 interface between chains.
- A–C · 956 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5K25 · Crystal structure of human phosphatase PRL-2 in complex with the ADP-bound Bateman domain… · the same entry in another collection · chain A against A, TM-score 1.00
- Q12974 · AlphaFold monomer V2.0 prediction for protein tyrosine phosphatase type iva 2 (Q12974) · a predicted model of the same protein · chain A against A, TM-score 0.94
- Q8NE01 · AlphaFold monomer V2.0 prediction for metal transporter CNNM3 (Q8NE01) · a predicted model of the same protein · chain C against A, TM-score 0.91
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 Q12974
- Every structure of UniProt Q8NE01
- Elsewhere: RCSB PDB 5K25 · PDBe 5K25 · UniProt Q12974 · UniProt Q8NE01
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