Research workbench
Crystal structure of cbr 703 bound to escherichia COLI RNA polymerase holoenzyme
Analyse Crystal structure of cbr 703 bound to escherichia COLI RNA polymerase holoenzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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