MolNFT v2 · #155888 · protein + DNA + RNA
Mycobacterium tuberculosis initial transcription complex comprising sigma H and 5'-OH RNA of 5 nt
6KON · DNA-directed RNA polymerase subunit alpha: “Mycobacterium tuberculosis initial transcription complex comprising sigma H and 5'-OH RNA of 5 nt”. X-ray diffraction at 3, 2 ligands (ZN, MG), 20 pockets (best druggability 0.86). MolNFT…
- PDB
- 6KON
- Type
- protein + DNA + RNA
- Length
- 3,091 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3
- Source
- Mycobacterium tuberculosis H37Rv; SYNTHETIC CONSTRUCT
- 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, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · resolution 3 · 9 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 216 | 21% helix, 41% strand | P9WGZ1 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 233 | 19% helix, 40% strand | P9WGZ1 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1092 | 25% helix, 26% strand | P9WGY9 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1252 | 45% helix, 14% strand | P9WGY7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 73 | 49% helix, 5% strand | P9WGY5 |
| F | ECF RNA polymerase sigma factor SigH | protein | 180 | 73% helix, 2% strand | P9WGH9 |
| G | DNA (5'-D(P*GP*TP*TP*GP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*C)-3') | dna | 23 | — | — |
| H | DNA (5'-D(P*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*GP*GP*GP*TP*G)-3') | dna | 17 | — | — |
| I | RNA (5'-R(*CP*UP*CP*GP*A)-3') | rna | 5 | — | — |
Ligands and binding sites
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 | 954 | 0.86 | 0.88 | 94 | empty |
| 2 | 1038 | 0.84 | 0.85 | 75 | empty |
| 3 | 737 | 0.82 | 0.86 | 100 | empty |
| 4 | 815 | 0.81 | 0.84 | 69 | empty |
| 5 | 846 | 0.80 | 0.82 | 92 | empty |
Interfaces
20 interfaces between chains.
- C–D · 8384 Ų buried · 101 hydrogen bonds · protein-protein
- D–E · 2121 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 2030 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 2022 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 2012 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6KON · Mycobacterium tuberculosis initial transcription complex comprising sigma H and 5'-oh RNA… · the same entry in another collection · chain I against I, 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 0.95
- 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 6KON · PDBe 6KON · UniProt P9WGZ1 · UniProt P9WGY9 · UniProt P9WGY7 · UniProt P9WGY5 · UniProt P9WGH9
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