Research workbench
Mycobacterium tuberculosis rnap open promoter complex with RBPA/CARD and AP3 promoter
Analyse Mycobacterium tuberculosis rnap open promoter complex with RBPA/CARD and AP3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EDT
- Type
- protein + DNA
- Length
- 3,646 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 0.86
Structure
electron microscopy · 10 distinct chains · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 225 | 19% helix, 36% strand | A5U8D3 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 237 | 19% helix, 31% 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 | 1270 | 43% helix, 13% strand | A5U053 |
| 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 | 322 | 67% helix, 2% strand | P9WGI0 |
| J | RNA polymerase-binding protein rbpa | protein | 109 | 23% helix, 18% strand | P9WHJ4 |
| O | DNA (65-mer) | dna | 65 | — | — |
| P | DNA (65-mer) | dna | 65 | — | — |
| M | RNA polymerase-binding transcription factor card | protein | 159 | 50% helix, 15% 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 | 938 | 0.86 | 0.88 | 107 | empty |
| 2 | 896 | 0.82 | 0.84 | 81 | empty |
| 3 | 831 | 0.82 | 0.84 | 65 | empty |
| 4 | 1119 | 0.81 | 0.83 | 103 | empty |
| 5 | 328 | 0.80 | 0.91 | 49 | empty |
Interfaces
26 interfaces between chains.
- C–D · 8552 Ų buried · 85 hydrogen bonds · protein-protein
- D–F · 2723 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2380 Ų buried · 8 hydrogen bonds · protein-protein
- O–P · 2337 Ų buried · 200 hydrogen bonds · nucleic-nucleic
- D–E · 2241 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6EDT · Mycobacterium tuberculosis RNAP open promoter complex with RbpA/CarD and AP3 promoter · the same entry in another collection · chain M against M, TM-score 1.00
- P9WJG2 · AlphaFold monomer V2.0 prediction for RNA polymerase-binding transcription factor card… · a predicted model of the same protein · chain M against A, TM-score 0.94
- 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 0.94
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 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 6EDT · PDBe 6EDT · UniProt A5U8D3 · UniProt V9Z879 · UniProt A5U053 · UniProt A0A0T9N9K3 · UniProt P9WGI0 · UniProt P9WHJ4 · UniProt P9WJG2
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