Research workbench
Structure of prl-1 in complex with the bateman domain of CNNM2
Analyse Structure of prl-1 in complex with the bateman domain of CNNM2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LXQ
- Type
- protein
- Length
- 602 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein tyrosine phosphatase type iva 1; Metal transporter CNNM2
- EC
- 3.1.3.48
- UniProt
- Q63739, Q3TWN3
- Ligands
- ATP, ZN
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C | Protein tyrosine phosphatase type iva 1 (EC 3.1.3.48) | protein | 151 | 44% helix, 19% strand | Q63739 |
| A, H | Metal transporter CNNM2 | protein | 150 | 39% helix, 27% strand | Q3TWN3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.65 | 0.76 | 42 | ATP, ZN |
| 2 | 286 | 0.61 | 0.79 | 31 | empty |
| 3 | 278 | 0.60 | 0.79 | 32 | empty |
| 4 | 149 | 0.58 | 0.82 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–H · 1517 Ų buried · 9 hydrogen bonds · protein-protein
- B–A · 507 Ų buried · 10 hydrogen bonds · protein-protein
- C–H · 500 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5LXQ · Structure of PRL-1 in complex with the Bateman domain of CNNM2 · the same entry in another collection · chain B against B, TM-score 1.00
- Q3TWN3 · AlphaFold monomer V2.0 prediction for metal transporter CNNM2 (Q3TWN3) · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q63739 · AlphaFold monomer V2.0 prediction for protein tyrosine phosphatase type iva 1 (Q63739) · a predicted model of the same protein · chain B 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 Q63739
- Every structure of UniProt Q3TWN3
- Elsewhere: RCSB PDB 5LXQ · PDBe 5LXQ · UniProt Q63739 · UniProt Q3TWN3
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