Research workbench
2.17 ångström crystal structure of DNA-directed RNA polymerase subunit alpha from campylobacter jejuni.
Analyse 2.17 ångström crystal structure of DNA-directed RNA polymerase subunit alpha… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NOI
- Type
- protein
- Length
- 446 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit alpha
- EC
- 2.7.7.6
- UniProt
- Q9PM80
- Ligands
- NA, CL, IOD
- Pockets
- 2 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 227 | 24% helix, 41% strand | Q9PM80 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 219 | 25% helix, 40% strand | Q9PM80 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 12 copies · chains A, B
- IOD · Iodide ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.37 | 0.78 | 14 | empty |
| 2 | 95 | 0.35 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2001 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 4NOI · 2.17 Angstrom Crystal Structure of DNA-directed RNA Polymerase Subunit Alpha from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9PM80 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (Q9PM80) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q9PM80
- Elsewhere: RCSB PDB 4NOI · PDBe 4NOI · UniProt Q9PM80
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