Research workbench
Mycobacterium tuberculosis wt rnap transcription open promoter complex with WHIB7 promoter
Analyse Mycobacterium tuberculosis wt rnap transcription open promoter complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KIN
- Type
- protein + DNA
- Length
- 3,612 residues
- Chains
- 10
- Method
- electron microscopy
- 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, A5U052, A0A045J9E2, A0A0T9N9K3, A0A0H3LGM9, P9WHJ4, P9WJG2
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 10 distinct chains · 36% helix, 19% 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, 37% strand | A5U8D3 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 237 | 19% helix, 35% strand | A5U8D3 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1111 | 25% helix, 25% strand | A5U052 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1270 | 43% helix, 14% strand | A0A045J9E2 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 83 | 45% helix, 5% strand | A0A0T9N9K3 |
| F | RNA polymerase sigma factor siga | protein | 317 | 67% helix, 2% strand | A0A0H3LGM9 |
| J | RNA polymerase-binding protein rbpa | protein | 107 | 24% helix, 23% strand | P9WHJ4 |
| M | RNA polymerase-binding transcription factor card | protein | 159 | 48% helix, 16% strand | P9WJG2 |
| O | DNA (54-mer) | dna | 54 | — | — |
| P | DNA (49-mer) | dna | 49 | — | — |
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 | 1030 | 0.83 | 0.84 | 123 | empty |
| 2 | 1096 | 0.82 | 0.83 | 88 | empty |
| 3 | 835 | 0.80 | 0.83 | 66 | empty |
| 4 | 374 | 0.78 | 0.87 | 49 | empty |
| 5 | 366 | 0.76 | 0.86 | 34 | empty |
Interfaces
25 interfaces between chains.
- C–D · 8332 Ų buried · 86 hydrogen bonds · protein-protein
- D–F · 2453 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2392 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 2161 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 2152 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 7KIN · Mycobacterium tuberculosis WT RNAP transcription open promoter complex with WhiB7 promoter · the same entry in another collection · chain P against P, TM-score 1.00
- A5U052 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (A5U052) · 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 A5U052
- Every structure of UniProt A0A045J9E2
- Every structure of UniProt A0A0T9N9K3
- Every structure of UniProt A0A0H3LGM9
- Every structure of UniProt P9WHJ4
- Every structure of UniProt P9WJG2
- Elsewhere: RCSB PDB 7KIN · PDBe 7KIN · UniProt A5U8D3 · UniProt A5U052 · UniProt A0A045J9E2 · UniProt A0A0T9N9K3 · UniProt A0A0H3LGM9 · UniProt P9WHJ4 · UniProt P9WJG2
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