MolNFT v1 · #155626 · protein + DNA + RNA
The cryo-EM structure of E. COLI cuer transcription activation complex
6LDI · DNA-directed RNA polymerase subunit alpha: “The cryo-EM structure of E. COLI cuer transcription activation complex”. Electron microscopy, 3 ligands (ZN, MG, AG), 20 pockets (best druggability 0.86). MolNFT v1 #155626 on GenesisL1…
- PDB
- 6LDI
- Type
- protein + DNA + RNA
- Length
- 4,027 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase subunit beta…
- EC
- 2.7.7.6
- UniProt
- P0A7Z4, P0A8V2, P0A8T7, P0A800, P00579, P0A9G4
- Ligands
- ZN, MG, AG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 11 distinct chains · 34% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 230 | 20% helix, 34% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 227 | 16% helix, 33% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1338 | 26% helix, 21% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1331 | 31% helix, 16% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 76 | 67% helix, 0% strand | P0A800 |
| F | RNA polymerase sigma factor rpod | protein | 465 | 64% helix, 1% strand | P00579 |
| 1 | DNA (50-mer) | dna | 50 | — | — |
| 2 | DNA (50-mer) | dna | 50 | — | — |
| 3 | RNA (5'-R(*CP*UP*CP*GP*A)-3') | rna | 5 | — | — |
| G | Hth-type transcriptional regulator cuer | protein | 127 | 54% helix, 2% strand | P0A9G4 |
| H | Hth-type transcriptional regulator cuer | protein | 128 | 62% helix, 2% strand | P0A9G4 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains D
- MG · Magnesium ion · metal · chains D, 3
- AG · Silver ion · metal · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 908 | 0.86 | 0.89 | 96 | empty |
| 2 | 905 | 0.84 | 0.87 | 82 | empty |
| 3 | 928 | 0.83 | 0.84 | 74 | empty |
| 4 | 593 | 0.82 | 0.88 | 78 | empty |
| 5 | 611 | 0.79 | 0.85 | 63 | empty |
Interfaces
27 interfaces between chains.
- C–D · 8320 Ų buried · 72 hydrogen bonds · protein-protein
- D–F · 2768 Ų buried · 15 hydrogen bonds · protein-protein
- C–F · 2211 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 1997 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1984 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6LDI · The cryo-EM structure of E. coli CueR transcription activation complex · the same entry in another collection · chain H against H, TM-score 1.00
- P0A8V2 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (P0A8V2) · a predicted model of the same protein · chain C against A, TM-score 0.99
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
- Every structure of UniProt P0A8V2
- Every structure of UniProt P0A8T7
- Every structure of UniProt P0A800
- Every structure of UniProt P00579
- Every structure of UniProt P0A9G4
- Elsewhere: RCSB PDB 6LDI · PDBe 6LDI · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P00579 · UniProt P0A9G4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.