Research workbench
Escherichia COLI rpob S531L mutant RNA polymerase holoenzyme in complex with kanglemycin a
Analyse Escherichia COLI rpob S531L mutant RNA polymerase holoenzyme 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
- 6CUX
- Type
- protein
- Length
- 6,973 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
- KNG, ZN, MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 12 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 227 | 22% helix, 36% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 214 | 19% helix, 32% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1339 | 30% helix, 23% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1166 | 43% helix, 13% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 89 | 64% helix, 0% strand | P0A800 |
| F | RNA polymerase sigma factor rpod | protein | 468 | 66% helix, 1% strand | P00579 |
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 224 | 20% helix, 30% strand | P0A7Z4 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 215 | 19% helix, 32% strand | P0A7Z4 |
| I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1328 | 31% helix, 23% strand | P0A8V2 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1155 | 43% helix, 14% strand | P0A8T7 |
| K | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 63% helix, 0% strand | P0A800 |
| L | RNA polymerase sigma factor rpod | protein | 469 | 65% helix, 3% strand | P00579 |
Ligands and binding sites
- KNG · Kanglemycin A · ligand · chains C, F
- 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 | 1149 | 0.84 | 0.85 | 105 | empty |
| 2 | 523 | 0.83 | 0.89 | 62 | empty |
| 3 | 588 | 0.81 | 0.87 | 68 | empty |
| 4 | 157 | 0.80 | 0.96 | 31 | empty |
| 5 | 477 | 0.78 | 0.85 | 53 | empty |
Interfaces
19 interfaces between chains.
- C–D · 8197 Ų buried · 108 hydrogen bonds · protein-protein
- I–J · 8171 Ų buried · 104 hydrogen bonds · protein-protein
- J–L · 2847 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 2798 Ų buried · 23 hydrogen bonds · protein-protein
- I–L · 2160 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6CUX · Escherichia coli RpoB S531L mutant RNA polymerase holoenzyme in complex with Kanglemycin A · 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 P0A7Z4
- Every structure of UniProt P0A8V2
- Every structure of UniProt P0A8T7
- Every structure of UniProt P0A800
- Every structure of UniProt P00579
- Elsewhere: RCSB PDB 6CUX · PDBe 6CUX · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P00579
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