MolNFT v1 · #110316 · protein
Crystal structure of cbr 703 bound to escherichia COLI RNA polymerase holoenzyme
4XSX · DNA-directed RNA polymerase subunit alpha: “Crystal structure of cbr 703 bound to escherichia COLI RNA polymerase holoenzyme”. X-ray diffraction, 3 ligands (42S, ZN, MG), 20 pockets (best druggability 0.83). MolNFT v1 #110316 on…
- PDB
- 4XSX
- 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, A8ARN6, P00579
- Ligands
- 42S, ZN, MG
- 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 | 224 | 18% helix, 35% strand | A7ZSI4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 220 | 18% helix, 28% strand | A7ZSI4 |
| C, I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 30% 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 | 64% helix, 0% strand | A8ARN6 |
| F | RNA polymerase sigma factor rpod | protein | 470 | 66% helix, 3% strand | P00579 |
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 228 | 18% helix, 34% strand | A7ZSI4 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 217 | 18% helix, 30% strand | A7ZSI4 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1236 | 40% helix, 15% strand | A7ZUK2 |
| K | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 63% helix, 0% strand | A8ARN6 |
| L | RNA polymerase sigma factor rpod | protein | 469 | 66% helix, 3% strand | P00579 |
Ligands and binding sites
- 42S · N'-hydroxy-N-phenyl-3-(trifluoromethyl)benzenecarboximidamide · 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 | 928 | 0.83 | 0.85 | 84 | empty |
| 2 | 807 | 0.82 | 0.85 | 74 | empty |
| 3 | 638 | 0.78 | 0.83 | 64 | empty |
| 4 | 1134 | 0.78 | 0.80 | 89 | empty |
| 5 | 576 | 0.77 | 0.84 | 60 | empty |
Interfaces
19 interfaces between chains.
- I–J · 8143 Ų buried · 101 hydrogen bonds · protein-protein
- C–D · 8119 Ų buried · 104 hydrogen bonds · protein-protein
- D–F · 2779 Ų buried · 24 hydrogen bonds · protein-protein
- J–L · 2774 Ų buried · 26 hydrogen bonds · protein-protein
- C–F · 2099 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4XSX · Crystal structure of CBR 703 bound to Escherichia coli RNA polymerase holoenzyme · the same entry in another collection · chain K against K, 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 A8ARN6
- Every structure of UniProt P00579
- Elsewhere: RCSB PDB 4XSX · PDBe 4XSX · UniProt A7ZSI4 · UniProt A7ZUK1 · UniProt A7ZUK2 · UniProt A8ARN6 · UniProt P00579
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