Research workbench
Structure of the E. COLI alpha C-terminal domain of RNA polymerase in complex with cap and DNA
Analyse Structure of the E. COLI alpha C-terminal domain of RNA polymerase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LB2
- Type
- protein + DNA
- Length
- 383 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- D(*CP*TP*TP*TP*TP*TP*TP*CP*CP*TP*AP*AP*AP*AP*TP*GP*TP*GP*AP *T)-3'; 5'…
- EC
- 2.7.7.6
- UniProt
- P0ACJ8, P0A7Z4
- Ligands
- CMP
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K | 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 | — | — |
| J | 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 | — | — |
| A | Catabolite gene activator protein | protein | 201 | 40% helix, 30% strand | P0ACJ8 |
| B | DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) | protein | 72 | 51% helix, 3% strand | P0A7Z4 |
| E | DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) | protein | 66 | 58% helix, 3% strand | P0A7Z4 |
Ligands and binding sites
- CMP · Adenosine-3',5'-cyclic-monophosphate · ligand · chains A
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 | 909 | 0.70 | 0.75 | 63 | empty |
| 2 | 68 | 0.69 | 0.96 | 17 | empty |
| 3 | 370 | 0.68 | 0.81 | 46 | CMP |
| 4 | 112 | 0.36 | 0.74 | 18 | empty |
| 5 | 71 | 0.36 | 0.78 | 20 | empty |
Interfaces
9 interfaces between chains.
- K–J · 865 Ų buried · 74 hydrogen bonds · nucleic-nucleic
- J–A · 434 Ų buried · 11 hydrogen bonds · protein-nucleic
- K–A · 403 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–B · 341 Ų buried · 8 hydrogen bonds · protein-protein
- K–E · 236 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 1LB2 · Structure of the E. coli alpha C-terminal domain of RNA polymerase in complex with CAP… · the same entry in another collection · chain K against K, 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 1LB2 · PDBe 1LB2 · UniProt P0ACJ8 · UniProt P0A7Z4
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