MolNFT v1 · #37953 · protein
Ctd-specific phosphatase SCP1 in complex with peptide C-terminal domain of RNA polymerase II
2GHQ · Carboxy-terminal domain RNA polymerase II polypeptide a…: “Ctd-specific phosphatase SCP1 in complex with peptide C-terminal domain of RNA polymerase II”. X-ray diffraction, 1 ligand (MG), 1 pocket (best druggability 0.33). MolNFT v1…
- PDB
- 2GHQ
- Type
- protein
- Length
- 374 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxy-terminal domain RNA polymerase II polypeptide a small phosphatase 1; DNA-directed…
- EC
- 3.1.3.16, 2.7.7.6
- UniProt
- Q9GZU7, P24928
- Ligands
- MG
- Pockets
- 1 · best druggability 0.33
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 24% 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 | 28% helix, 26% strand | Q9GZU7 |
| C | DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6) | protein | 5 | 0% helix, 0% strand | P24928 |
| D | DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6) | protein | 9 | 0% helix, 0% strand | P24928 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B, D, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.33 | 0.79 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–D · 683 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 378 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 26 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 2GHQ · CTD-specific phosphatase Scp1 in complex with peptide C-terminal domain of RNA polymerase… · the same entry in another collection · chain D against D, 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
- P24928 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase II subunit RPB1 (P24928) · a predicted model of the same protein · chain C against A, TM-score 0.77
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
- Every structure of UniProt P24928
- Elsewhere: RCSB PDB 2GHQ · PDBe 2GHQ · UniProt Q9GZU7 · UniProt P24928
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