Research workbench
The crystal structure of a large insert in RNA polymerase (rpoc) subunit from E. COLI
Analyse The crystal structure of a large insert in RNA polymerase (rpoc) subunit from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IQZ
- Type
- protein
- Length
- 851 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit beta'
- EC
- 2.7.7.6
- UniProt
- P0A8T7
- Ligands
- NA, IOD
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 2% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 178 | 3% helix, 42% strand | P0A8T7 |
| B | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 176 | 2% helix, 45% strand | P0A8T7 |
| C | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 176 | 2% helix, 43% strand | P0A8T7 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 146 | 0% helix, 42% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 175 | 3% helix, 44% strand | P0A8T7 |
Ligands and binding sites
- NA · Sodium ion · metal · 7 copies · chains A, D, B, C, E
- IOD · Iodide ion · ion · 56 copies · chains A, D, E, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.75 | 0.84 | 84 | IOD |
| 2 | 304 | 0.73 | 0.86 | 56 | IOD |
| 3 | 479 | 0.68 | 0.79 | 65 | IOD |
| 4 | 255 | 0.54 | 0.77 | 43 | IOD |
| 5 | 136 | 0.42 | 0.75 | 29 | IOD |
Interfaces
5 interfaces between chains.
- A–D · 1183 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1139 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 837 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 447 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 202 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 4IQZ · The crystal structure of a large insert in RNA polymerase (RpoC) subunit from E. coli · the same entry in another collection · chain E against E, TM-score 1.00
- P0A8T7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (P0A8T7) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 P0A8T7
- Elsewhere: RCSB PDB 4IQZ · PDBe 4IQZ · UniProt P0A8T7
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