Research workbench
Crystal structure of E. COLI RNA polymerase alpha subunit C-terminal domain
Analyse Crystal structure of E. COLI RNA polymerase alpha subunit C-terminal domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K4G
- Type
- protein
- Length
- 668 residues
- Chains
- 8
- 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
- P0A7Z4
- Ligands
- NA
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F, G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 84 | 48% helix, 8% strand | P0A7Z4 |
| B, D, E, H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 83 | 46% helix, 7% strand | P0A7Z4 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 783 | 0.72 | 0.78 | 83 | empty |
| 2 | 499 | 0.68 | 0.79 | 58 | empty |
| 3 | 222 | 0.57 | 0.79 | 30 | empty |
| 4 | 145 | 0.50 | 0.79 | 20 | empty |
| 5 | 165 | 0.48 | 0.76 | 29 | empty |
Interfaces
14 interfaces between chains.
- G–H · 1397 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1390 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1387 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1379 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 403 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified (methylation).
Compared structures
- 3K4G · Crystal structure of E. coli RNA polymerase alpha subunit C-terminal domain · the same entry in another collection · chain A against A, TM-score 1.00
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 P0A7Z4
- Elsewhere: RCSB PDB 3K4G · PDBe 3K4G · UniProt P0A7Z4
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