MolNFT v1 · #110318 · protein
Crystal structure of cbr 9393 bound to escherichia COLI RNA polymerase holoenzyme
4XSZ · DNA-directed RNA polymerase subunit alpha: “Crystal structure of cbr 9393 bound to escherichia COLI RNA polymerase holoenzyme”. X-ray diffraction, 3 ligands (42U, ZN, MG), 20 pockets (best druggability 0.82). MolNFT v1 #110318 on…
- PDB
- 4XSZ
- Type
- protein
- Length
- 7,078 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, B1IYV1, P00579
- Ligands
- 42U, ZN, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 11 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 224 | 21% helix, 35% strand | A7ZSI4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 220 | 18% helix, 30% strand | A7ZSI4 |
| C, I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 29% helix, 23% strand | A7ZUK1 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1166 | 42% helix, 14% strand | A7ZUK2 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 89 | 67% helix, 0% strand | B1IYV1 |
| F | RNA polymerase sigma factor rpod | protein | 470 | 64% helix, 3% strand | P00579 |
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 228 | 20% helix, 35% strand | A7ZSI4 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 217 | 18% helix, 31% strand | A7ZSI4 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1236 | 39% helix, 15% strand | A7ZUK2 |
| K | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 61% helix, 0% strand | B1IYV1 |
| L | RNA polymerase sigma factor rpod | protein | 469 | 65% helix, 3% strand | P00579 |
Ligands and binding sites
- 42U · 4-[3-(4-fluorophenyl)-1H-pyrazol-4-yl]-N-[2-(piperazin-1-yl)ethyl]-2-(trifluoromethyl)aniline · ligand · 2 copies · chains C, D, I, J
- ZN · Zinc ion · metal · 4 copies · chains D, J
- MG · Magnesium ion · metal · 2 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 | 593 | 0.82 | 0.87 | 70 | empty |
| 2 | 578 | 0.82 | 0.87 | 67 | empty |
| 3 | 1030 | 0.81 | 0.82 | 105 | empty |
| 4 | 848 | 0.79 | 0.82 | 81 | empty |
| 5 | 578 | 0.78 | 0.84 | 52 | empty |
Interfaces
19 interfaces between chains.
- I–J · 8134 Ų buried · 110 hydrogen bonds · protein-protein
- C–D · 8108 Ų buried · 110 hydrogen bonds · protein-protein
- J–L · 2826 Ų buried · 29 hydrogen bonds · protein-protein
- D–F · 2816 Ų buried · 29 hydrogen bonds · protein-protein
- C–F · 2122 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4XSZ · Crystal structure of CBR 9393 bound to Escherichia coli RNA polymerase holoenzyme · 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 B1IYV1
- Every structure of UniProt P00579
- Elsewhere: RCSB PDB 4XSZ · PDBe 4XSZ · UniProt A7ZSI4 · UniProt A7ZUK1 · UniProt A7ZUK2 · UniProt B1IYV1 · UniProt P00579
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