MolNFT v1 · #114878 · protein
Crystal structure of the saccharomyces cerevisiae RTR1 (regulator of transcription)
5C2Y · RNA polymerase II subunit B1 ctd phosphatase RTR1: “Crystal structure of the saccharomyces cerevisiae RTR1 (regulator of transcription)”. X-ray diffraction, 2 ligands (ZN, SO4), 4 pockets (best druggability 0.81). MolNFT v1 #114878…
- PDB
- 5C2Y
- Type
- protein
- Length
- 346 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA polymerase II subunit B1 ctd phosphatase RTR1
- EC
- 3.1.3.16
- UniProt
- P40084
- Ligands
- ZN, SO4
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA polymerase II subunit B1 ctd phosphatase RTR1 (EC 3.1.3.16) | protein | 178 | 56% helix, 1% strand | P40084 |
| B | RNA polymerase II subunit B1 ctd phosphatase RTR1 (EC 3.1.3.16) | protein | 168 | 54% helix, 1% strand | P40084 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 782 | 0.81 | 0.84 | 69 | SO4 |
| 2 | 167 | 0.52 | 0.79 | 41 | empty |
| 3 | 53 | 0.30 | 0.76 | 12 | empty |
| 4 | 50 | 0.28 | 0.75 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 1172 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- P40084 · AlphaFold monomer V2.0 prediction for RNA polymerase II subunit B1 ctd phosphatase RTR1… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P40084
- Elsewhere: RCSB PDB 5C2Y · PDBe 5C2Y · UniProt P40084
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