MolNFT v1 · #147475 · protein + DNA
Mycobacterium tuberculosis rnap promoter unwinding intermediate complex with RBPA/CARD and AP3 promoter
6EE8 · DNA-directed RNA polymerase subunit alpha: “Mycobacterium tuberculosis rnap promoter unwinding intermediate complex with RBPA/CARD and AP3 promoter”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.81).…
- PDB
- 6EE8
- Type
- protein + DNA
- Length
- 3,633 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, V9Z879, A5U053, A0A0T9N9K3, P9WGI0, P9WHJ4, P9WJG2
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 10 distinct chains · 37% 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 | 18% helix, 39% strand | A5U8D3 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 237 | 19% helix, 34% strand | A5U8D3 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1111 | 25% helix, 24% strand | V9Z879 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1266 | 44% helix, 14% strand | A5U053 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 83 | 46% helix, 5% strand | A0A0T9N9K3 |
| F | RNA polymerase sigma factor siga | protein | 319 | 68% helix, 2% strand | P9WGI0 |
| J | RNA polymerase-binding protein rbpa | protein | 108 | 23% helix, 22% strand | P9WHJ4 |
| O | DNA (65-mer) | dna | 65 | — | — |
| P | DNA (60-mer) | dna | 60 | — | — |
| M | RNA polymerase-binding transcription factor card | protein | 159 | 48% helix, 16% strand | P9WJG2 |
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 | 836 | 0.81 | 0.84 | 71 | empty |
| 2 | 909 | 0.80 | 0.82 | 98 | empty |
| 3 | 1128 | 0.79 | 0.81 | 99 | empty |
| 4 | 477 | 0.78 | 0.86 | 61 | empty |
| 5 | 534 | 0.78 | 0.85 | 58 | empty |
Interfaces
25 interfaces between chains.
- C–D · 8387 Ų buried · 79 hydrogen bonds · protein-protein
- O–P · 2559 Ų buried · 240 hydrogen bonds · nucleic-nucleic
- D–F · 2471 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2403 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 2257 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6EE8 · Mycobacterium tuberculosis RNAP promoter unwinding intermediate complex with RbpA/CarD… · the same entry in another collection · chain M against M, TM-score 1.00
- A5U053 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (A5U053) · a predicted model of the same protein · chain D against A, TM-score 0.97
- 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 0.93
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 V9Z879
- Every structure of UniProt A5U053
- Every structure of UniProt A0A0T9N9K3
- Every structure of UniProt P9WGI0
- Every structure of UniProt P9WHJ4
- Every structure of UniProt P9WJG2
- Elsewhere: RCSB PDB 6EE8 · PDBe 6EE8 · UniProt A5U8D3 · UniProt V9Z879 · UniProt A5U053 · UniProt A0A0T9N9K3 · UniProt P9WGI0 · UniProt P9WHJ4 · UniProt P9WJG2
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