Research workbench
Crystal structure of mycobacterium tuberculosis transcription initiation COMPLEX(ECF sigma factor L) containing 5NT RNA with 4NT spacer
Analyse Crystal structure of mycobacterium tuberculosis transcription initiation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DV9
- Type
- protein + DNA + RNA
- Length
- 3,148 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, P9WGH5
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.84
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 | 225 | 20% helix, 40% strand | P9WGZ1 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 233 | 21% helix, 40% strand | P9WGZ1 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1126 | 26% helix, 27% strand | P9WGY9 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1265 | 45% helix, 14% strand | P9WGY7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 81 | 46% helix, 1% strand | P9WGY5 |
| F | Ecf RNA polymerase sigma factor sigl | protein | 174 | 73% helix, 2% strand | P9WGH5 |
| I | RNA (5'-R(*CP*UP*CP*GP*A)-3') | rna | 5 | — | — |
| G | DNA (5'- D(*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*GP*G)-3') | dna | 17 | — | — |
| H | DNA (5'- D(P*CP*GP*TP*GP*TP*CP*AP*GP*AP*GP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*C) -3') | dna | 22 | — | — |
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 | 998 | 0.84 | 0.85 | 106 | empty |
| 2 | 1193 | 0.83 | 0.84 | 115 | empty |
| 3 | 1130 | 0.83 | 0.84 | 117 | empty |
| 4 | 654 | 0.81 | 0.85 | 79 | empty |
| 5 | 447 | 0.80 | 0.89 | 43 | empty |
Interfaces
20 interfaces between chains.
- C–D · 8648 Ų buried · 120 hydrogen bonds · protein-protein
- A–B · 2476 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 2292 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 2149 Ų buried · 33 hydrogen bonds · protein-protein
- D–F · 2126 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6DV9 · Crystal structure of Mycobacterium tuberculosis transcription initiation complex(ECF… · 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 0.94
- 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 0.92
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 P9WGH5
- Elsewhere: RCSB PDB 6DV9 · PDBe 6DV9 · UniProt P9WGZ1 · UniProt P9WGY9 · UniProt P9WGY7 · UniProt P9WGY5 · UniProt P9WGH5
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