Research workbench
Mycobacterium tuberculosis RNA polymerase sigma L holoenzyme open promoter complex containing tnp-2198
Analyse Mycobacterium tuberculosis RNA polymerase sigma L holoenzyme open promoter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RWI
- Type
- protein + DNA
- Length
- 3,141 residues
- Chains
- 8
- 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
- Ligands
- 7US
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 8 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 | 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 | 1126 | 26% helix, 28% strand | P9WGY8 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1264 | 45% helix, 14% strand | A0A045J9E2 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 81 | 46% helix, 1% strand | A0A045H2R3 |
| F | RNA polymerase sigma factor | protein | 174 | 73% helix, 2% strand | A0A045IR27 |
| G | T DNA | dna | 15 | — | — |
| H | Nt DNA | dna | 24 | — | — |
Ligands and binding sites
- 7US · (3am,9s,10bp,14s,15r,16s,17r,18r,19r,20s,21s,25r)-6,18, 20-trihydroxy-14-methoxy-7,9,15,17,19,21,25-heptamethyl-1'-[2-(2-methyl-5-nitro-1H-imidazol-1-yl) ethyl]-5,10,26-trioxo-3,5,9,10-tetrahydrospiro[9,4-(epoxypentadecanoimino)furo[2',3':7,8]naphtho[1,2-d]imidazole-2,4'-piperidin]-16-yl acetate · ligand · chains C, G
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 | 1001 | 0.86 | 0.87 | 103 | empty |
| 2 | 964 | 0.82 | 0.83 | 99 | empty |
| 3 | 786 | 0.80 | 0.84 | 69 | empty |
| 4 | 580 | 0.80 | 0.86 | 63 | empty |
| 5 | 1031 | 0.77 | 0.79 | 114 | empty |
Interfaces
16 interfaces between chains.
- C–D · 8557 Ų buried · 109 hydrogen bonds · protein-protein
- A–B · 2469 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 2207 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 2131 Ų buried · 30 hydrogen bonds · protein-protein
- D–F · 2070 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 7RWI · Mycobacterium tuberculosis RNA polymerase sigma L holoenzyme open promoter complex… · the same entry in another collection · chain H against H, 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 0.98
- 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 7RWI · PDBe 7RWI · UniProt A5U8D3 · UniProt P9WGY8 · UniProt A0A045J9E2 · UniProt A0A045H2R3 · UniProt A0A045IR27
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.