MolNFT v1 · #115416 · protein + DNA
E. COLI RNA polymerase alpha subunit ctd in complex with cap and DNA: A(5)-tract binding site for alpha ctd
5CIZ · Camp-activated global transcriptional regulator crp: “E. COLI RNA polymerase alpha subunit ctd in complex with cap and DNA: A(5)-tract binding site for alpha ctd”. X-ray diffraction, 1 ligand (CMP), 7 pockets (best druggability…
- PDB
- 5CIZ
- Type
- protein + DNA
- Length
- 321 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-activated global transcriptional regulator crp; DNA-directed RNA polymerase subunit…
- EC
- 2.7.7.6
- UniProt
- P0ACJ8, P0A7Z4
- Ligands
- CMP
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-activated global transcriptional regulator crp | protein | 203 | 38% helix, 30% strand | P0ACJ8 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 74 | 51% helix, 3% strand | P0A7Z4 |
| D | DNA (5'- D(*CP*TP*TP*TP*TP*TP*GP*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*CP*AP*AP*AP*AP* AP*G)-3') | dna | 24 | — | — |
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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 805 | 0.75 | 0.79 | 92 | CMP |
| 2 | 102 | 0.35 | 0.74 | 17 | empty |
| 3 | 67 | 0.35 | 0.78 | 14 | empty |
| 4 | 53 | 0.29 | 0.76 | 13 | empty |
| 5 | 62 | 0.29 | 0.74 | 13 | empty |
Interfaces
6 interfaces between chains.
- D–E · 882 Ų buried · 65 hydrogen bonds · nucleic-nucleic
- A–E · 444 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–D · 387 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–B · 349 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 250 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 5CIZ · E. coli RNA polymerase alpha subunit CTD in complex with CAP and DNA: A(5)-tract binding… · 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 5CIZ · PDBe 5CIZ · UniProt P0ACJ8 · UniProt P0A7Z4
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