Research workbench
Mycobacterium tuberculosis rnap HOLO/RBPA/FIDAXOMICIN
Analyse Mycobacterium tuberculosis rnap HOLO/RBPA/FIDAXOMICIN in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C06
- Type
- protein
- Length
- 3,353 residues
- Chains
- 7
- 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 0.89
Structure
electron microscopy · 7 distinct chains · 32% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 226 | 13% helix, 21% strand | A0A045J8T1 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 237 | 16% helix, 19% strand | A0A045J8T1 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1111 | 23% helix, 13% strand | V9Z879 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1263 | 38% helix, 7% strand | A0A045J9E2 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 83 | 43% helix, 2% strand | A0A0T9N9K3 |
| F | RNA polymerase sigma factor siga | protein | 326 | 63% helix, 2% strand | A0A045HD00 |
| J | RNA polymerase-binding protein rbpa | protein | 107 | 20% helix, 12% strand | A0A045IP01 |
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 C, 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 | 970 | 0.89 | 0.91 | 152 | empty |
| 2 | 724 | 0.89 | 0.93 | 138 | empty |
| 3 | 784 | 0.88 | 0.91 | 134 | empty |
| 4 | 1056 | 0.87 | 0.88 | 139 | empty |
| 5 | 715 | 0.87 | 0.90 | 90 | empty |
Interfaces
13 interfaces between chains.
- C–D · 5373 Ų buried · 98 hydrogen bonds · protein-protein
- A–B · 1918 Ų buried · 31 hydrogen bonds · protein-protein
- D–E · 1663 Ų buried · 42 hydrogen bonds · protein-protein
- D–F · 1626 Ų buried · 33 hydrogen bonds · protein-protein
- F–J · 1470 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6C06 · Mycobacterium tuberculosis RNAP Holo/RbpA/Fidaxomicin · 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 6C06 · PDBe 6C06 · UniProt A0A045J8T1 · UniProt V9Z879 · UniProt A0A045J9E2 · UniProt A0A0T9N9K3 · UniProt A0A045HD00 · UniProt A0A045IP01
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.