MolNFT v1 · #111064 · protein
Escherichia COLI RNA polymerase in complex with squaramide compound 8.
4YFK · DNA-directed RNA polymerase subunit alpha: “Escherichia COLI RNA polymerase in complex with squaramide compound 8.”. X-ray diffraction, 3 ligands (4C6, MG, ZN), 20 pockets (best druggability 0.83). MolNFT v1 #111064 on GenesisL1: 3D…
- PDB
- 4YFK
- Type
- protein
- Length
- 7,079 residues
- Chains
- 12
- Method
- x-ray diffraction
- 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
- A7ZSI4, A7ZUK1, A7ZUK2, A7ZTK1, P00579
- Ligands
- 4C6, MG, ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 11 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 319 | 26% helix, 25% strand | A7ZSI4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 217 | 19% helix, 32% strand | A7ZSI4 |
| C, I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 29% helix, 24% strand | A7ZUK1 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1163 | 43% helix, 14% strand | A7ZUK2 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 89 | 60% helix, 0% strand | A7ZTK1 |
| F | RNA polymerase sigma factor rpod | protein | 468 | 63% helix, 3% strand | P00579 |
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 227 | 20% helix, 35% strand | A7ZSI4 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 216 | 18% helix, 36% strand | A7ZSI4 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1152 | 42% helix, 14% strand | A7ZUK2 |
| K | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 59% helix, 0% strand | A7ZTK1 |
| L | RNA polymerase sigma factor rpod | protein | 469 | 66% helix, 3% strand | P00579 |
Ligands and binding sites
- 4C6 · 3,5-dimethyl-N-{2-[4-(4-methylbenzyl)piperidin-1-yl]-3,4-dioxocyclobut-1-en-1-yl}-1,2-oxazole-4-sulfonamide · ligand · 2 copies · chains C, D, I, J
- MG · Magnesium ion · metal · 4 copies · chains C, D, I, J
- ZN · Zinc ion · metal · 4 copies · chains D, J
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 | 972 | 0.83 | 0.84 | 95 | empty |
| 2 | 997 | 0.82 | 0.83 | 69 | 4C6 |
| 3 | 578 | 0.81 | 0.87 | 73 | empty |
| 4 | 930 | 0.81 | 0.83 | 81 | 4C6 |
| 5 | 959 | 0.81 | 0.83 | 102 | empty |
Interfaces
21 interfaces between chains.
- I–J · 8056 Ų buried · 92 hydrogen bonds · protein-protein
- C–D · 8016 Ų buried · 96 hydrogen bonds · protein-protein
- J–L · 2727 Ų buried · 27 hydrogen bonds · protein-protein
- D–F · 2664 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2154 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4YFK · Escherichia coli RNA polymerase in complex with squaramide compound 8. · the same entry in another collection · chain L against L, TM-score 1.00
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 A7ZSI4
- Every structure of UniProt A7ZUK1
- Every structure of UniProt A7ZUK2
- Every structure of UniProt A7ZTK1
- Every structure of UniProt P00579
- Elsewhere: RCSB PDB 4YFK · PDBe 4YFK · UniProt A7ZSI4 · UniProt A7ZUK1 · UniProt A7ZUK2 · UniProt A7ZTK1 · UniProt P00579
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