Research workbench
Clostridioides difficile rnap with fidaxomicin
Analyse Clostridioides difficile rnap with fidaxomicin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L7B
- Type
- protein
- Length
- 3,125 residues
- Chains
- 6
- 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
- Q18CI5, Q18CF1, Q18CF3, Q182S6, A0A500XEZ5
- Ligands
- FI8, ZN, MG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 6 distinct chains · 34% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 224 | 20% helix, 29% strand | Q18CI5 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 237 | 17% helix, 29% strand | Q18CI5 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1166 | 28% helix, 21% strand | Q18CF1 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1148 | 39% helix, 11% strand | Q18CF3 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 78 | 49% helix, 3% strand | Q182S6 |
| F | RNA polymerase sigma factor siga | protein | 272 | 64% helix, 1% strand | A0A500XEZ5 |
Ligands and binding sites
- FI8 · Fidaxomicin · ligand · chains C, D, F
- 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 | 921 | 0.81 | 0.83 | 76 | FI8 |
| 2 | 777 | 0.80 | 0.84 | 71 | empty |
| 3 | 797 | 0.76 | 0.81 | 95 | empty |
| 4 | 798 | 0.75 | 0.79 | 66 | empty |
| 5 | 952 | 0.75 | 0.78 | 83 | empty |
Interfaces
10 interfaces between chains.
- C–D · 8333 Ų buried · 85 hydrogen bonds · protein-protein
- D–F · 2423 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2197 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 2072 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1827 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 7L7B · Clostridioides difficile RNAP with fidaxomicin · the same entry in another collection · chain F against F, TM-score 1.00
- Q18CF1 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (Q18CF1) · a predicted model of the same protein · chain C against A, TM-score 0.98
- Q18CF3 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (Q18CF3) · a predicted model of the same protein · chain D against A, TM-score 0.97
- Q18CI5 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (Q18CI5) · a predicted model of the same protein · chain A against A, TM-score 0.94
- Q182S6 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (Q182S6) · a predicted model of the same protein · chain E against A, TM-score 0.91
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 Q18CI5
- Every structure of UniProt Q18CF1
- Every structure of UniProt Q18CF3
- Every structure of UniProt Q182S6
- Every structure of UniProt A0A500XEZ5
- Elsewhere: RCSB PDB 7L7B · PDBe 7L7B · UniProt Q18CI5 · UniProt Q18CF1 · UniProt Q18CF3 · UniProt Q182S6 · UniProt A0A500XEZ5
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