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Crystal structure of mtb sigma L transcription initiation complex with 5 nt long RNA primer
Analyse Crystal structure of mtb sigma L transcription initiation complex with 5 nt… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TYE
- Type
- protein + DNA + RNA
- Length
- 3,122 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA polymerase sigma factor; DNA (5'- D(*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*AP*TP*CP*GP*AP*GP*G…
- EC
- 2.7.7.6
- UniProt
- A0A045IR27, A5U8D3, P9WGY8, A0A0E8TXU5, A0A045H2R3
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 9 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | RNA polymerase sigma factor | protein | 163 | 68% helix, 2% strand | A0A045IR27 |
| G | DNA (5'- D(*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*AP*TP*CP*GP*AP*GP*G)-3') | dna | 17 | — | — |
| H | DNA (5'- D(P*GP*TP*GP*TP*CP*AP*GP*TP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP *C)-3') | dna | 23 | — | — |
| I | RNA (5'-R(P*CP*UP*CP*GP*A)-3') | rna | 5 | — | — |
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 225 | 21% helix, 40% strand | A5U8D3 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 232 | 22% helix, 38% strand | A5U8D3 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1114 | 27% helix, 28% strand | P9WGY8 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1262 | 45% helix, 13% strand | A0A0E8TXU5 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 81 | 46% helix, 1% strand | A0A045H2R3 |
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 | 949 | 0.86 | 0.88 | 100 | empty |
| 2 | 815 | 0.84 | 0.87 | 89 | empty |
| 3 | 1127 | 0.82 | 0.83 | 107 | empty |
| 4 | 380 | 0.77 | 0.88 | 43 | empty |
| 5 | 352 | 0.76 | 0.87 | 33 | empty |
Interfaces
19 interfaces between chains.
- C–D · 8188 Ų buried · 112 hydrogen bonds · protein-protein
- A–B · 2515 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 2256 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 2166 Ų buried · 33 hydrogen bonds · protein-protein
- F–D · 1952 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 6TYE · Crystal structure of MTB sigma L transcription initiation complex with 5 nt long RNA… · the same entry in another collection · chain E against E, TM-score 1.00
- P9WGY8 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (P9WGY8) · a predicted model of the same protein · chain C against A, TM-score 0.99
- A5U8D3 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (A5U8D3) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 A0A045IR27
- Every structure of UniProt A5U8D3
- Every structure of UniProt P9WGY8
- Every structure of UniProt A0A0E8TXU5
- Every structure of UniProt A0A045H2R3
- Elsewhere: RCSB PDB 6TYE · PDBe 6TYE · UniProt A0A045IR27 · UniProt A5U8D3 · UniProt P9WGY8 · UniProt A0A0E8TXU5 · UniProt A0A045H2R3
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