MolNFT v1 · #142216 · protein
Mycobacterium tuberculosis RNA polymerase holoenzyme with ecf sigma factor sigma H
5ZX3 · DNA-directed RNA polymerase subunit alpha: “Mycobacterium tuberculosis RNA polymerase holoenzyme with ecf sigma factor sigma H”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.86). MolNFT v1 #142216 on GenesisL1…
- PDB
- 5ZX3
- Type
- protein
- Length
- 3,063 residues
- Chains
- 6
- 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
- P9WGZ1, P9WGY9, P9WGY7, P9WGY5, P9WGH9
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 221 | 19% helix, 38% strand | P9WGZ1 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 231 | 20% helix, 41% strand | P9WGZ1 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1105 | 27% helix, 27% strand | P9WGY9 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1257 | 45% helix, 16% strand | P9WGY7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 76 | 50% helix, 5% strand | P9WGY5 |
| F | Ecf RNA polymerase sigma factor sigh | protein | 173 | 72% helix, 2% strand | P9WGH9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · 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 | 802 | 0.86 | 0.88 | 74 | empty |
| 2 | 835 | 0.84 | 0.87 | 107 | empty |
| 3 | 1080 | 0.84 | 0.85 | 121 | empty |
| 4 | 350 | 0.78 | 0.88 | 33 | empty |
| 5 | 1059 | 0.76 | 0.78 | 131 | empty |
Interfaces
10 interfaces between chains.
- C–D · 8712 Ų buried · 119 hydrogen bonds · protein-protein
- A–B · 2341 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 2173 Ų buried · 30 hydrogen bonds · protein-protein
- D–E · 2164 Ų buried · 32 hydrogen bonds · protein-protein
- C–F · 1971 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5ZX3 · Mycobacterium tuberculosis RNA polymerase holoenzyme with ECF sigma factor sigma H · 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 0.99
- 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 0.96
- P9WGZ1 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (P9WGZ1) · a predicted model of the same protein · chain A against A, TM-score 0.94
- 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 0.92
- P9WGH9 · AlphaFold monomer V2.0 prediction for ecf RNA polymerase sigma factor sigh (P9WGH9) · a predicted model of the same protein · chain F against A, TM-score 0.44
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 P9WGH9
- Elsewhere: RCSB PDB 5ZX3 · PDBe 5ZX3 · UniProt P9WGZ1 · UniProt P9WGY9 · UniProt P9WGY7 · UniProt P9WGY5 · UniProt P9WGH9
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