Research workbench
Cryo-EM structure of bacillus subtilis RNA polymerase in complex with held
Analyse Cryo-EM structure of bacillus subtilis RNA polymerase in complex with held in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WVK
- Type
- protein
- Length
- 3,631 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, 3.6.4.12
- UniProt
- P20429, P37870, P37871, O31718, O35011, O32215
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 6 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 224 | 23% helix, 44% strand | P20429 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1099 | 23% helix, 27% strand | P37870 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1184 | 39% helix, 14% strand | P37871 |
| E | UPF0356 protein ykzg | protein | 69 | 25% helix, 32% strand | O31718 |
| F | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 61 | 54% helix, 3% strand | O35011 |
| H | DNA helicase IV (EC 3.6.4.12) | protein | 770 | 45% helix, 15% strand | O32215 |
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 | 756 | 0.85 | 0.88 | 97 | empty |
| 2 | 1111 | 0.84 | 0.85 | 136 | empty |
| 3 | 676 | 0.81 | 0.85 | 70 | empty |
| 4 | 725 | 0.80 | 0.84 | 114 | empty |
| 5 | 527 | 0.78 | 0.85 | 67 | empty |
Interfaces
14 interfaces between chains.
- C–D · 7425 Ų buried · 73 hydrogen bonds · protein-protein
- D–H · 3951 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 1641 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1629 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 1548 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6WVK · Cryo-EM structure of Bacillus subtilis RNA Polymerase in complex with HelD · the same entry in another collection · chain H against H, TM-score 1.00
- P37870 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (P37870) · a predicted model of the same protein · chain C against A, TM-score 0.96
- O31718 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit epsilon (O31718) · a predicted model of the same protein · chain E against A, TM-score 0.95
- P20429 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (P20429) · a predicted model of the same protein · chain A against A, TM-score 0.91
- O35011 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (O35011) · a predicted model of the same protein · chain F against A, TM-score 0.91
- P37871 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (P37871) · a predicted model of the same protein · chain D against A, TM-score 0.84
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 P20429
- Every structure of UniProt P37870
- Every structure of UniProt P37871
- Every structure of UniProt O31718
- Every structure of UniProt O35011
- Every structure of UniProt O32215
- Elsewhere: RCSB PDB 6WVK · PDBe 6WVK · UniProt P20429 · UniProt P37870 · UniProt P37871 · UniProt O31718 · UniProt O35011 · UniProt O32215
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