Research workbench
Mycobacterium tuberculosis RNA polymerase transcription initiation complex with ecf sigma factor sigma H and 7NT RNA
Analyse Mycobacterium tuberculosis RNA polymerase transcription initiation complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZX2
- Type
- protein + DNA + RNA
- Length
- 3,199 residues
- Chains
- 9
- 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 0.87
Structure
x-ray diffraction · 9 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 215 | 21% helix, 40% strand | P9WGZ1 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 234 | 21% helix, 41% strand | P9WGZ1 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1137 | 26% helix, 26% strand | P9WGY9 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1260 | 45% helix, 15% strand | P9WGY7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 76 | 53% helix, 5% strand | P9WGY5 |
| F | Ecf RNA polymerase sigma factor sigh | protein | 175 | 74% helix, 2% strand | P9WGH9 |
| G | DNA (48-mer) | dna | 48 | — | — |
| H | DNA (47-mer) | dna | 47 | — | — |
| I | RNA (5'-R(*CP*CP*CP*UP*CP*GP*A)-3') | rna | 7 | — | — |
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 | 1054 | 0.87 | 0.88 | 101 | empty |
| 2 | 1049 | 0.87 | 0.88 | 97 | empty |
| 3 | 1021 | 0.83 | 0.84 | 110 | empty |
| 4 | 615 | 0.81 | 0.87 | 51 | empty |
| 5 | 655 | 0.80 | 0.85 | 69 | empty |
Interfaces
21 interfaces between chains.
- C–D · 8963 Ų buried · 121 hydrogen bonds · protein-protein
- D–E · 2215 Ų buried · 28 hydrogen bonds · protein-protein
- D–F · 2088 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 2080 Ų buried · 34 hydrogen bonds · protein-protein
- C–F · 1985 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5ZX2 · Mycobacterium tuberculosis RNA polymerase transcription initiation complex with ECF sigma… · the same entry in another collection · chain H against H, 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
- 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 0.95
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 5ZX2 · PDBe 5ZX2 · UniProt P9WGZ1 · UniProt P9WGY9 · UniProt P9WGY7 · UniProt P9WGY5 · UniProt P9WGH9
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