MolNFT v1 · #148617 · protein
Single particle cryo EM structure of mycobacterium tuberculosis RNA polymerase in complex with fidaxomicin
6FBV · DNA-directed RNA polymerase subunit alpha: “Single particle cryo EM structure of mycobacterium tuberculosis RNA polymerase in complex with fidaxomicin”. Electron microscopy, 3 ligands (FI8, ZN, MG), 20 pockets (best druggability…
- PDB
- 6FBV
- Type
- protein
- Length
- 3,217 residues
- Chains
- 6
- Method
- electron microscopy
- 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
- P9WGZ1, P9WGY9, P9WGY7, P9WGY5, P9WGI1
- Ligands
- FI8, ZN, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 223 | 21% helix, 38% strand | P9WGZ1 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 230 | 22% helix, 37% strand | P9WGZ1 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1118 | 26% helix, 26% strand | P9WGY9 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1270 | 43% helix, 14% strand | P9WGY7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 83 | 46% helix, 5% strand | P9WGY5 |
| F | RNA polymerase sigma factor siga | protein | 293 | 66% helix, 1% strand | P9WGI1 |
Ligands and binding sites
- FI8 · Fidaxomicin · ligand · chains C, D, F
- ZN · Zinc ion · metal · 2 copies · chains D
- MG · Magnesium ion · metal · chains D
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 | 675 | 0.82 | 0.87 | 89 | empty |
| 2 | 808 | 0.79 | 0.82 | 92 | empty |
| 3 | 707 | 0.77 | 0.82 | 80 | empty |
| 4 | 517 | 0.76 | 0.84 | 46 | FI8 |
| 5 | 356 | 0.76 | 0.86 | 36 | empty |
Interfaces
10 interfaces between chains.
- C–D · 7921 Ų buried · 83 hydrogen bonds · protein-protein
- D–F · 2478 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2298 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 2232 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1879 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6FBV · Single particle cryo em structure of Mycobacterium tuberculosis RNA polymerase in complex… · the same entry in another collection · chain F against F, TM-score 1.00
- P9WGY9 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (P9WGY9) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P9WGY7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (P9WGY7) · a predicted model of the same protein · chain D against A, TM-score 0.95
- P9WGY5 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (P9WGY5) · a predicted model of the same protein · chain E against A, TM-score 0.92
- P9WGI1 · AlphaFold monomer V2.0 prediction for RNA polymerase sigma factor siga (P9WGI1) · a predicted model of the same protein · chain F against A, TM-score 0.82
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 P9WGZ1
- Every structure of UniProt P9WGY9
- Every structure of UniProt P9WGY7
- Every structure of UniProt P9WGY5
- Every structure of UniProt P9WGI1
- Elsewhere: RCSB PDB 6FBV · PDBe 6FBV · UniProt P9WGZ1 · UniProt P9WGY9 · UniProt P9WGY7 · UniProt P9WGY5 · UniProt P9WGI1
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