Research workbench
Mycobacterium tuberculosis RNA polymerase transcription initiation open complex with a chimeric ecf sigma factor SIGH/E
Analyse Mycobacterium tuberculosis RNA polymerase transcription initiation open complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JCY
- Type
- protein + DNA + RNA
- Length
- 3,140 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, P9WGG7
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 9 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, 43% strand | P9WGZ1 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 231 | 19% helix, 39% strand | P9WGZ1 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1139 | 27% helix, 27% 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 | 54% helix, 5% strand | P9WGY5 |
| F | Ecf RNA polymerase sigma factor SIGH,ECF RNA polymerase sigma factor SIGE,ECF RNA polymerase sigma factor sigh | protein | 164 | 71% helix, 2% strand | P9WGH9, P9WGG7 |
| 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*T)-3') | dna | 20 | — | — |
| I | RNA (5'-R(*CP*CP*UP*CP*GP*A)-3') | rna | 6 | — | — |
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 | 1173 | 0.85 | 0.86 | 97 | empty |
| 2 | 931 | 0.82 | 0.84 | 75 | empty |
| 3 | 670 | 0.81 | 0.86 | 85 | empty |
| 4 | 501 | 0.81 | 0.88 | 66 | empty |
| 5 | 665 | 0.80 | 0.84 | 75 | empty |
Interfaces
21 interfaces between chains.
- C–D · 8470 Ų buried · 97 hydrogen bonds · protein-protein
- A–B · 2231 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 2107 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 2005 Ų buried · 28 hydrogen bonds · protein-protein
- D–F · 1783 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6JCY · Mycobacterium tuberculosis RNA polymerase transcription initiation open complex with a… · 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 0.97
- 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
- Every structure of UniProt P9WGG7
- Elsewhere: RCSB PDB 6JCY · PDBe 6JCY · UniProt P9WGZ1 · UniProt P9WGY9 · UniProt P9WGY7 · UniProt P9WGY5 · UniProt P9WGH9 · UniProt P9WGG7
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