Research workbench
Crystal structure of the complex between phosphatase prl-2 in the oxidized state with the bateman domain of murine magnesium transporter CNNM3
Analyse Crystal structure of the complex between phosphatase prl-2 in the oxidized… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K24
- Type
- protein
- Length
- 573 residues
- Chains
- 4
- 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
- O70274, Q32NY4
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein tyrosine phosphatase type iva 2 (EC 3.1.3.48) | protein | 152 | 42% helix, 16% strand | O70274 |
| B | Protein tyrosine phosphatase type iva 2 (EC 3.1.3.48) | protein | 149 | 44% helix, 17% strand | O70274 |
| C | Metal transporter CNNM3 | protein | 137 | 33% helix, 30% strand | Q32NY4 |
| D | Metal transporter CNNM3 | protein | 135 | 35% helix, 30% strand | Q32NY4 |
Ligands and binding sites
- FLC · Citrate anion · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.70 | 0.81 | 56 | empty |
| 2 | 449 | 0.59 | 0.74 | 45 | empty |
| 3 | 141 | 0.58 | 0.83 | 21 | empty |
| 4 | 119 | 0.37 | 0.73 | 22 | empty |
| 5 | 78 | 0.37 | 0.76 | 11 | empty |
Interfaces
3 interfaces between chains.
- C–D · 801 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 604 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 540 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5K24 · Crystal structure of the complex between phosphatase PRL-2 in the oxidized state with the… · the same entry in another collection · chain D against D, TM-score 1.00
- O70274 · AlphaFold monomer V2.0 prediction for protein tyrosine phosphatase type iva 2 (O70274) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q32NY4 · AlphaFold monomer V2.0 prediction for metal transporter CNNM3 (Q32NY4) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 O70274
- Every structure of UniProt Q32NY4
- Elsewhere: RCSB PDB 5K24 · PDBe 5K24 · UniProt O70274 · UniProt Q32NY4
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