MolNFT v1 · #165529 · protein + DNA + RNA
Crystal structure of mtb sigma L transcription initiation complex with 6 nt long RNA primer
6TYF · DNA-directed RNA polymerase subunit alpha: “Crystal structure of mtb sigma L transcription initiation complex with 6 nt long RNA primer”. X-ray diffraction, 20 pockets (best druggability 0.85). MolNFT v1 #165529 on GenesisL1: 3D…
- PDB
- 6TYF
- Type
- protein + DNA + RNA
- Length
- 3,136 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
- A5U8D3, P9WGY8, A0A045J9E2, A0A045H2R3, A0A045IR27
- 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 | 225 | 17% helix, 40% strand | A5U8D3 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 232 | 20% helix, 38% strand | A5U8D3 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1114 | 26% helix, 28% strand | P9WGY8 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1262 | 45% helix, 14% strand | A0A045J9E2 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 81 | 46% helix, 1% strand | A0A045H2R3 |
| G | DNA (5'- D(*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*AP*TP*CP*GP*AP*GP*GP*GP*T)-3') | dna | 19 | — | — |
| 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*CP*UP*CP*GP*A)-3') | rna | 6 | — | — |
| F | RNA polymerase sigma factor | protein | 174 | 73% helix, 2% strand | A0A045IR27 |
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 | 846 | 0.85 | 0.87 | 103 | empty |
| 2 | 908 | 0.82 | 0.84 | 83 | empty |
| 3 | 397 | 0.81 | 0.90 | 46 | empty |
| 4 | 571 | 0.80 | 0.86 | 90 | empty |
| 5 | 371 | 0.77 | 0.87 | 35 | empty |
Interfaces
21 interfaces between chains.
- C–D · 8092 Ų buried · 111 hydrogen bonds · protein-protein
- A–B · 2467 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 2240 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 2145 Ų buried · 28 hydrogen bonds · protein-protein
- D–F · 2047 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 6TYF · Crystal structure of MTB sigma L transcription initiation complex with 6 nt long RNA… · the same entry in another collection · chain F against F, 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 A5U8D3
- Every structure of UniProt P9WGY8
- Every structure of UniProt A0A045J9E2
- Every structure of UniProt A0A045H2R3
- Every structure of UniProt A0A045IR27
- Elsewhere: RCSB PDB 6TYF · PDBe 6TYF · UniProt A5U8D3 · UniProt P9WGY8 · UniProt A0A045J9E2 · UniProt A0A045H2R3 · UniProt A0A045IR27
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