Research workbench
X-ray crystal structure of the escherichia COLI RNA polymerase in complex with benzoxazinorifamycin-2B
Analyse X-ray crystal structure of the escherichia COLI RNA polymerase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KN4
- Type
- protein
- Length
- 7,121 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
- P0A7Z4, P0A8V2, P0A8T7, P0A800, P00579
- Ligands
- 1RL, ZN, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 10 distinct chains · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 323 | 25% helix, 23% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 221 | 19% helix, 38% strand | P0A7Z4 |
| C, H | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1335 | 28% helix, 19% strand | P0A8V2 |
| D, I | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1160 | 39% helix, 11% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 90 | 64% helix, 0% strand | P0A800 |
| X | RNA polymerase sigma factor rpod | protein | 517 | 64% helix, 0% strand | P00579 |
| F | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 229 | 19% helix, 29% strand | P0A7Z4 |
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 217 | 19% helix, 37% strand | P0A7Z4 |
| J | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 76 | 63% helix, 0% strand | P0A800 |
| Y | RNA polymerase sigma factor rpod | protein | 458 | 67% helix, 0% strand | P00579 |
Ligands and binding sites
- 1RL · Benzoxazinorifamycin-2b · ligand · 2 copies · chains C, X, H, Y
- ZN · Zinc ion · metal · 4 copies · chains D, I
- MG · Magnesium ion · metal · 2 copies · chains D, H, I
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 | 1151 | 0.87 | 0.88 | 132 | empty |
| 2 | 1135 | 0.87 | 0.88 | 134 | empty |
| 3 | 628 | 0.80 | 0.85 | 80 | empty |
| 4 | 339 | 0.78 | 0.89 | 52 | empty |
| 5 | 888 | 0.78 | 0.81 | 89 | empty |
Interfaces
22 interfaces between chains.
- H–I · 8111 Ų buried · 94 hydrogen bonds · protein-protein
- C–D · 8045 Ų buried · 100 hydrogen bonds · protein-protein
- D–X · 3620 Ų buried · 36 hydrogen bonds · protein-protein
- I–Y · 2837 Ų buried · 27 hydrogen bonds · protein-protein
- C–X · 2260 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4KN4 · X-ray crystal structure of the Escherichia coli RNA polymerase in complex with… · the same entry in another collection · chain Y against Y, 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 P0A7Z4
- Every structure of UniProt P0A8V2
- Every structure of UniProt P0A8T7
- Every structure of UniProt P0A800
- Every structure of UniProt P00579
- Elsewhere: RCSB PDB 4KN4 · PDBe 4KN4 · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P00579
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