Research workbench
Mtb rnap HOLO/RBPA/FIDAXOMICIN/UPSTREAM fork DNA
Analyse Mtb rnap HOLO/RBPA/FIDAXOMICIN/UPSTREAM fork DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BZO
- Type
- protein + DNA
- Length
- 3,410 residues
- Chains
- 9
- 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
- A0A045J8T1, V9Z879, A0A045J9E2, A0A0T9N9K3, A0A045HD00, A0A045IP01
- Ligands
- FI8, ZN, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 9 distinct chains · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 226 | 19% helix, 35% strand | A0A045J8T1 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 237 | 17% helix, 29% strand | A0A045J8T1 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1111 | 21% helix, 24% strand | V9Z879 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1263 | 44% helix, 13% strand | A0A045J9E2 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 83 | 40% helix, 5% strand | A0A0T9N9K3 |
| F | RNA polymerase sigma factor siga | protein | 326 | 69% helix, 2% strand | A0A045HD00 |
| J | RNA polymerase-binding protein rbpa | protein | 107 | 22% helix, 23% strand | A0A045IP01 |
| O | DNA (32-mer) | dna | 31 | — | — |
| P | DNA (26-mer) | dna | 26 | — | — |
Ligands and binding sites
- FI8 · Fidaxomicin · ligand · chains C, D, F, J
- ZN · Zinc ion · metal · 2 copies · chains D
- MG · Magnesium ion · metal · chains D
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 | 807 | 0.85 | 0.87 | 95 | FI8 |
| 2 | 812 | 0.80 | 0.83 | 83 | empty |
| 3 | 927 | 0.79 | 0.82 | 93 | empty |
| 4 | 739 | 0.75 | 0.80 | 76 | empty |
| 5 | 379 | 0.75 | 0.86 | 34 | empty |
Interfaces
19 interfaces between chains.
- C–D · 7922 Ų buried · 72 hydrogen bonds · protein-protein
- D–F · 2516 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2423 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 2179 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1984 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 6BZO · Mtb RNAP Holo/RbpA/Fidaxomicin/upstream fork DNA · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A045J8T1
- Every structure of UniProt V9Z879
- Every structure of UniProt A0A045J9E2
- Every structure of UniProt A0A0T9N9K3
- Every structure of UniProt A0A045HD00
- Every structure of UniProt A0A045IP01
- Elsewhere: RCSB PDB 6BZO · PDBe 6BZO · UniProt A0A045J8T1 · UniProt V9Z879 · UniProt A0A045J9E2 · UniProt A0A0T9N9K3 · UniProt A0A045HD00 · UniProt A0A045IP01
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