MolNFT v1 · #135820 · protein
Escherichia COLI RNA polymerase and rifampin complex, rpob D516V mutant
5UAH · DNA-directed RNA polymerase subunit alpha: “Escherichia COLI RNA polymerase and rifampin complex, rpob D516V mutant”. X-ray diffraction, 3 ligands (RFP, MG, ZN), 20 pockets (best druggability 0.84). MolNFT v1 #135820 on GenesisL1…
- PDB
- 5UAH
- Type
- protein
- Length
- 7,000 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
- RFP, MG, ZN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 11 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 233 | 20% helix, 32% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 217 | 20% helix, 32% strand | P0A7Z4 |
| C, I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 31% helix, 23% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1167 | 42% helix, 14% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 89 | 66% helix, 0% strand | P0A800 |
| F | RNA polymerase sigma factor rpod | protein | 468 | 69% helix, 3% strand | P00579 |
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 227 | 18% helix, 33% strand | P0A7Z4 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 216 | 19% helix, 31% strand | P0A7Z4 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1155 | 42% helix, 13% strand | P0A8T7 |
| K | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 62% helix, 0% strand | P0A800 |
| L | RNA polymerase sigma factor rpod | protein | 469 | 68% helix, 3% strand | P00579 |
Ligands and binding sites
- RFP · Rifampicin · ligand · chains C
- MG · Magnesium ion · metal · 4 copies · chains C, D, I, J
- ZN · Zinc ion · metal · 4 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 | 559 | 0.84 | 0.89 | 60 | empty |
| 2 | 654 | 0.84 | 0.88 | 71 | empty |
| 3 | 219 | 0.81 | 0.93 | 45 | empty |
| 4 | 949 | 0.80 | 0.82 | 108 | empty |
| 5 | 291 | 0.80 | 0.91 | 42 | empty |
Interfaces
20 interfaces between chains.
- C–D · 8244 Ų buried · 90 hydrogen bonds · protein-protein
- I–J · 8149 Ų buried · 87 hydrogen bonds · protein-protein
- J–L · 2815 Ų buried · 23 hydrogen bonds · protein-protein
- D–F · 2813 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2152 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5UAH · Escherichia coli RNA polymerase and Rifampin complex, RpoB D516V mutant · 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 5UAH · PDBe 5UAH · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P00579
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