MolNFT v1 · #69766 · protein
Crystal structure of SCP1 phosphatase D206A mutant phosphoryl- intermediate
3L0B · Carboxy-terminal domain RNA polymerase II polypeptide a…: “Crystal structure of SCP1 phosphatase D206A mutant phosphoryl- intermediate”. X-ray diffraction, 2 ligands (1PG, MG), 3 pockets (best druggability 0.56). MolNFT v1 #69766 on…
- PDB
- 3L0B
- Type
- protein
- Length
- 360 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxy-terminal domain RNA polymerase II polypeptide a small phosphatase 1
- EC
- 3.1.3.16
- UniProt
- Q9GZU7
- Ligands
- 1PG, MG
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Carboxy-terminal domain RNA polymerase II polypeptide a small phosphatase 1 (EC 3.1.3.16) | protein | 180 | 30% helix, 28% strand | Q9GZU7 |
Ligands and binding sites
- 1PG · 2-(2-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.56 | 0.76 | 40 | empty |
| 2 | 142 | 0.41 | 0.74 | 24 | 1PG |
| 3 | 132 | 0.38 | 0.73 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 399 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 3L0B · Crystal structure of SCP1 phosphatase D206A mutant phosphoryl-intermediate · the same entry in another collection · chain A against A, TM-score 1.00
- Q9GZU7 · AlphaFold monomer V2.0 prediction for carboxy-terminal domain RNA polymerase II… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9GZU7
- Elsewhere: RCSB PDB 3L0B · PDBe 3L0B · UniProt Q9GZU7
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