Research workbench
Mycobacterium tuberculosis initial transcription complex comprising sigma H and 5'-oh RNA of 9 nt
Analyse Mycobacterium tuberculosis initial transcription complex comprising sigma H and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KOP
- Type
- protein + DNA + RNA
- Length
- 3,133 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 | 218 | 20% helix, 40% strand | P9WGZ1 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 227 | 20% helix, 38% strand | P9WGZ1 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1138 | 25% helix, 26% strand | P9WGY9 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1263 | 45% helix, 13% strand | P9WGY7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 75 | 44% helix, 5% strand | P9WGY5 |
| F | Ecf RNA polymerase sigma factor sigh | protein | 159 | 72% helix, 0% 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 | 21 | — | — |
| I | RNA (5'-R(*CP*AP*CP*CP*CP*UP*CP*GP*A)-3') | rna | 9 | — | — |
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 | 740 | 0.85 | 0.89 | 94 | empty |
| 2 | 1076 | 0.83 | 0.85 | 119 | empty |
| 3 | 886 | 0.82 | 0.85 | 80 | empty |
| 4 | 922 | 0.81 | 0.83 | 102 | empty |
| 5 | 381 | 0.80 | 0.89 | 59 | empty |
Interfaces
18 interfaces between chains.
- C–D · 8329 Ų buried · 96 hydrogen bonds · protein-protein
- D–E · 2127 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 2089 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1969 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 1684 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6KOP · Mycobacterium tuberculosis initial transcription complex comprising sigma H and 5'-OH RNA… · the same entry in another collection · chain B against B, 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
- 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
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 6KOP · PDBe 6KOP · UniProt P9WGZ1 · UniProt P9WGY9 · UniProt P9WGY7 · UniProt P9WGY5 · UniProt P9WGH9
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