MolNFT v1 · #171745 · protein
Structure of the B. subtilis RNA polymerase in complex with held (dimer)
6ZFB · DNA-directed RNA polymerase subunit delta: “Structure of the B. subtilis RNA polymerase in complex with held (dimer)”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.83). MolNFT v1 #171745 on GenesisL1: 3D…
- PDB
- 6ZFB
- Type
- protein
- Length
- 7,313 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit delta; RNA polymerase subunit omega; DNA-directed RNA…
- EC
- 2.7.7.6, 3.6.4.12
- UniProt
- A0A410WI33, A0A063XB83, A0A2J0WBQ0, A0A063XB23, A0A164TSE8
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 8 distinct chains · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, d | DNA-directed RNA polymerase subunit delta | protein | 139 | 58% helix, 4% strand | — |
| E, e | RNA polymerase subunit omega | protein | 69 | 23% helix, 28% strand | A0A410WI33 |
| U, u | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 231 | 26% helix, 27% strand | A0A063XB83 |
| V, v | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 227 | 23% helix, 21% strand | A0A063XB83 |
| X | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1093 | 26% helix, 24% strand | A0A2J0WBQ0 |
| Y, y | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1127 | 41% helix, 10% strand | A0A063XB23 |
| H, h | DNA helicase (EC 3.6.4.12) | protein | 771 | 49% helix, 8% strand | A0A164TSE8 |
| x | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1092 | 25% helix, 23% strand | A0A2J0WBQ0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains Y, y
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 | 839 | 0.83 | 0.85 | 94 | empty |
| 2 | 1028 | 0.82 | 0.83 | 101 | empty |
| 3 | 678 | 0.81 | 0.85 | 92 | empty |
| 4 | 1064 | 0.81 | 0.82 | 105 | empty |
| 5 | 1135 | 0.81 | 0.82 | 101 | empty |
Interfaces
34 interfaces between chains.
- x–y · 5689 Ų buried · 42 hydrogen bonds · protein-protein
- X–Y · 5623 Ų buried · 40 hydrogen bonds · protein-protein
- y–h · 4523 Ų buried · 32 hydrogen bonds · protein-protein
- Y–H · 4484 Ų buried · 30 hydrogen bonds · protein-protein
- u–v · 2026 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6ZFB · Structure of the B. subtilis RNA POLYMERASE in complex with HelD (dimer) · the same entry in another collection · chain D against D, 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 A0A410WI33
- Every structure of UniProt A0A063XB83
- Every structure of UniProt A0A2J0WBQ0
- Every structure of UniProt A0A063XB23
- Every structure of UniProt A0A164TSE8
- Elsewhere: RCSB PDB 6ZFB · PDBe 6ZFB · UniProt A0A410WI33 · UniProt A0A063XB83 · UniProt A0A2J0WBQ0 · UniProt A0A063XB23 · UniProt A0A164TSE8
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