MolNFT v1 · #154859 · protein + DNA + RNA
Mycobacterium tuberculosis initial transcription complex comprising sigma H and 5'-oh RNA of 7 nt
6KOO · DNA-directed RNA polymerase subunit alpha: “Mycobacterium tuberculosis initial transcription complex comprising sigma H and 5'-oh RNA of 7 nt”. X-ray diffraction, 2 ligands (ZN, MG), 20 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 6KOO
- Type
- protein + DNA + RNA
- Length
- 3,147 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, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 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 | 217 | 19% helix, 41% strand | P9WGZ1 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 230 | 19% helix, 37% strand | P9WGZ1 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1135 | 27% helix, 25% strand | P9WGY9 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1258 | 45% helix, 14% strand | P9WGY7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 75 | 49% helix, 5% strand | P9WGY5 |
| F | Ecf RNA polymerase sigma factor sigh | protein | 182 | 71% helix, 2% strand | P9WGH9 |
| G | DNA (5'- D(*TP*TP*GP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP* a)-3') | dna | 23 | — | — |
| H | DNA (5'- D(*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*GP*GP*GP*TP*G)- 3') | dna | 20 | — | — |
| I | RNA (5'-R(*CP*CP*CP*UP*CP*GP*A)-3') | rna | 7 | — | — |
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 | 675 | 0.85 | 0.89 | 50 | empty |
| 2 | 1049 | 0.83 | 0.84 | 106 | empty |
| 3 | 426 | 0.83 | 0.91 | 53 | empty |
| 4 | 985 | 0.82 | 0.83 | 98 | empty |
| 5 | 376 | 0.82 | 0.91 | 49 | empty |
Interfaces
21 interfaces between chains.
- C–D · 8868 Ų buried · 102 hydrogen bonds · protein-protein
- C–F · 2433 Ų buried · 27 hydrogen bonds · protein-protein
- D–E · 2191 Ų buried · 21 hydrogen bonds · protein-protein
- D–F · 2165 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 2143 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 6KOO · 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 0.94
- 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 0.91
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 6KOO · PDBe 6KOO · UniProt P9WGZ1 · UniProt P9WGY9 · UniProt P9WGY7 · UniProt P9WGY5 · UniProt P9WGH9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.