MolNFT v1 · #137580 · protein + RNA
Escherichia COLI 6S RNA derivative in complex with escherichia COLI RNA polymerase SIGMA70-holoenzyme
5VT0 · DNA-directed RNA polymerase subunit alpha: “Escherichia COLI 6S RNA derivative in complex with escherichia COLI RNA polymerase SIGMA70-holoenzyme”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.84). MolNFT…
- PDB
- 5VT0
- Type
- protein + RNA
- Length
- 3,781 residues
- Chains
- 7
- 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
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 7 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 228 | 21% helix, 39% strand | P0A7Z4 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 217 | 18% helix, 31% strand | P0A7Z4 |
| I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 29% helix, 22% strand | P0A8V2 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1334 | 35% helix, 16% strand | P0A8T7 |
| K | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 59% helix, 0% strand | P0A800 |
| L | RNA polymerase sigma factor rpod | protein | 471 | 68% helix, 3% strand | P00579 |
| R | Escherichia COLI 6S RNA derivative (112-mer) | rna | 112 | — | — |
Ligands and binding sites
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 | 966 | 0.84 | 0.86 | 113 | empty |
| 2 | 731 | 0.83 | 0.87 | 84 | empty |
| 3 | 977 | 0.80 | 0.82 | 96 | empty |
| 4 | 760 | 0.80 | 0.84 | 73 | empty |
| 5 | 807 | 0.79 | 0.83 | 98 | empty |
Interfaces
12 interfaces between chains.
- I–J · 8422 Ų buried · 98 hydrogen bonds · protein-protein
- J–L · 2797 Ų buried · 29 hydrogen bonds · protein-protein
- I–L · 2327 Ų buried · 14 hydrogen bonds · protein-protein
- L–R · 2243 Ų buried · 30 hydrogen bonds · protein-nucleic
- G–I · 2003 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5VT0 · Escherichia coli 6S RNA derivative in complex with Escherichia coli RNA polymerase… · the same entry in another collection · chain R against R, 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 I against A, TM-score 0.99
- P0A8T7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (P0A8T7) · a predicted model of the same protein · chain J against A, TM-score 0.94
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
- Elsewhere: RCSB PDB 5VT0 · PDBe 5VT0 · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P00579
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