Research workbench
Structure of Nrd1 CID bound to phosphorylated RNAP II CTD
Analyse Structure of Nrd1 CID bound to phosphorylated RNAP II CTD in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2LO6
- Type
- protein
- Length
- 168 residues
- Chains
- 2
- Method
- solution nmr
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- NOT
- Source
- Saccharomyces cerevisiae S288c; SYNTHETIC CONSTRUCT
- Molecule
- Protein NRD1; DNA-directed RNA polymerase II subunit RPB1
- EC
- 2.7.7.6
- UniProt
- P53617, P04050
- Pockets
- 2 · best druggability 0.54
Structure
solution nmr · resolution NOT · 2 distinct chains · 63% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein NRD1 | protein | 154 | 68% helix, 0% strand | P53617 |
| B | DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6) | protein | 14 | 0% helix, 0% strand | P04050 |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.54 | 0.81 | 18 | empty |
| 2 | 63 | 0.31 | 0.75 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 560 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 2LO6 · Structure of NRD1 cid bound to phosphorylated rnap II ctd · the same entry in another collection · chain A against A, TM-score 1.00
- P53617 · AlphaFold monomer V2.0 prediction for protein NRD1 (P53617) · a predicted model of the same protein · chain A against A, TM-score 0.83
- P04050 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase II subunit RPB1 (P04050) · a predicted model of the same protein · chain B against A, TM-score 0.25
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 P53617
- Every structure of UniProt P04050
- Elsewhere: RCSB PDB 2LO6 · PDBe 2LO6 · UniProt P53617 · UniProt P04050
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