MolNFT v1 · #101670 · protein
Orthorhombic crystal form of PIR1 dual specificity phosphatase core
4NYH · RNA/RNP complex-1-interacting phosphatase: “Orthorhombic crystal form of PIR1 dual specificity phosphatase core”. X-ray diffraction, 2 ligands (PO4, CL), 7 pockets (best druggability 0.83). MolNFT v1 #101670 on GenesisL1: 3D…
- PDB
- 4NYH
- Type
- protein
- Length
- 541 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA/RNP complex-1-interacting phosphatase
- EC
- 3.1.3.-
- UniProt
- O75319
- Ligands
- PO4, CL
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA/RNP complex-1-interacting phosphatase (EC 3.1.3.-) | protein | 182 | 42% helix, 10% strand | O75319 |
| C | RNA/RNP complex-1-interacting phosphatase (EC 3.1.3.-) | protein | 177 | 44% helix, 11% strand | O75319 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.83 | 0.84 | 80 | PO4 |
| 2 | 51 | 0.36 | 0.80 | 15 | empty |
| 3 | 84 | 0.34 | 0.74 | 15 | empty |
| 4 | 87 | 0.33 | 0.74 | 17 | empty |
| 5 | 77 | 0.32 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- B–C · 672 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 606 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 503 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4NYH · Orthorhombic crystal form of pir1 dual specificity phosphatase core · the same entry in another collection · chain A against A, TM-score 1.00
- O75319 · AlphaFold monomer V2.0 prediction for RNA/RNP complex-1-interacting phosphatase (O75319) · a predicted model of the same protein · chain C 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 O75319
- Elsewhere: RCSB PDB 4NYH · PDBe 4NYH · UniProt O75319
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