Research workbench
E. COLI RNA polymerase alpha subunit C-terminal domain in complex with cap and DNA
Analyse E. COLI RNA polymerase alpha subunit C-terminal domain in complex with cap and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N4M
- Type
- protein + DNA
- Length
- 394 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catabolite gene activator; DNA-directed RNA polymerase subunit alpha; DNA (5'…
- EC
- 2.7.7.6
- UniProt
- P0ACJ8, P0A7Z4
- Ligands
- CMP
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Catabolite gene activator | protein | 203 | 38% helix, 30% strand | P0ACJ8 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 74 | 50% helix, 3% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 73 | 51% helix, 3% strand | P0A7Z4 |
| D | DNA (5'- D(*CP*TP*TP*TP*TP*TP*TP*CP*CP*TP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3') | dna | 20 | — | — |
| E | DNA (5'- D(*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP* AP*G)-3') | dna | 24 | — | — |
Ligands and binding sites
- CMP · Adenosine-3',5'-cyclic-monophosphate · ligand · 2 copies · chains A, D, E
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
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 | 400 | 0.70 | 0.82 | 44 | CMP |
| 2 | 579 | 0.62 | 0.74 | 33 | empty |
| 3 | 385 | 0.61 | 0.77 | 36 | empty |
| 4 | 98 | 0.53 | 0.84 | 25 | empty |
| 5 | 105 | 0.41 | 0.77 | 22 | empty |
Interfaces
9 interfaces between chains.
- D–E · 891 Ų buried · 63 hydrogen bonds · nucleic-nucleic
- A–E · 432 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–D · 362 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–B · 360 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 239 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 3N4M · E. coli RNA polymerase alpha subunit C-terminal domain in complex with CAP and DNA · the same entry in another collection · chain A against A, TM-score 1.00
- P0ACJ8 · AlphaFold monomer V2.0 prediction for camp-activated global transcriptional regulator crp… · a predicted model of the same protein · chain A 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 P0ACJ8
- Every structure of UniProt P0A7Z4
- Elsewhere: RCSB PDB 3N4M · PDBe 3N4M · UniProt P0ACJ8 · UniProt P0A7Z4
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