MolNFT v2 · #214961 · protein + DNA + RNA
The cryo-EM map of open TIEA-TEC complex
8K5A · DNA-directed RNA polymerase subunit alpha: “The cryo-EM map of open TIEA-TEC complex”. Electron microscopy at 3.3, 20 pockets (best druggability 0.84). MolNFT v2 #214961 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 8K5A
- Type
- protein + DNA + RNA
- Length
- 3,416 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.3
- Source
- Escherichia coli K-12; Escherichia phage T4
- Molecule
- DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase subunit beta…
- EC
- 2.7.7.6
- UniProt
- P0A7Z4, P0A8V2, P0A8T7, P0A800, P07879
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · resolution 3.3 · 9 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 230 | 22% helix, 39% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 228 | 23% helix, 35% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 32% helix, 23% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1352 | 35% helix, 17% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 76 | 61% helix, 0% strand | P0A800 |
| G | 15 kDa RNA polymerase-binding protein | protein | 129 | 53% helix, 5% strand | P07879 |
| H | DNA (29-mer) | dna | 29 | — | — |
| I | DNA (29-mer) | dna | 22 | — | — |
| J | RNA (5'-R(*CP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3') | rna | 10 | — | — |
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 | 1115 | 0.84 | 0.85 | 101 | empty |
| 2 | 598 | 0.81 | 0.87 | 82 | empty |
| 3 | 633 | 0.81 | 0.86 | 53 | empty |
| 4 | 975 | 0.80 | 0.82 | 89 | empty |
| 5 | 940 | 0.80 | 0.82 | 90 | empty |
Interfaces
16 interfaces between chains.
- C–D · 8481 Ų buried · 97 hydrogen bonds · protein-protein
- A–B · 2238 Ų buried · 21 hydrogen bonds · protein-protein
- D–G · 2015 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 1933 Ų buried · 27 hydrogen bonds · protein-protein
- D–E · 1384 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 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 0.96
- P0A8T7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (P0A8T7) · a predicted model of the same protein · chain D against A, TM-score 0.88
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 P07879
- Elsewhere: RCSB PDB 8K5A · PDBe 8K5A · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P07879
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