Research workbench
N-terminal domain of delta-subunit of RNA polymerase complexed with I3C and nickel ions
Analyse N-terminal domain of delta-subunit of RNA polymerase complexed with I3C and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NC7
- Type
- protein
- Length
- 158 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit delta
- UniProt
- P12464
- Ligands
- I3C, NI
- Pockets
- 1 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 62% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA-directed RNA polymerase subunit delta | protein | 79 | 62% helix, 0% strand | P12464 |
Ligands and binding sites
- I3C · 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid · ligand · chains A
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.69 | 0.78 | 45 | empty |
Interfaces
1 interface between chains.
- A–B · 443 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4NC7 · N-terminal domain of delta-subunit of RNA polymerase complexed with I3C and nickel ions · the same entry in another collection · chain A against A, TM-score 1.00
- P12464 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit delta (P12464) · a predicted model of the same protein · chain A against A, TM-score 0.84
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 P12464
- Elsewhere: RCSB PDB 4NC7 · PDBe 4NC7 · UniProt P12464
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