MolNFT v1 · #171657 · protein
Structure of the B. subtilis RNA polymerase in complex with held (monomer)
6ZCA · Probable DNA-directed RNA polymerase subunit DELTA,PROBABLE…: “Structure of the B. subtilis RNA polymerase in complex with held (monomer)”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.85). MolNFT v1 #171657…
- PDB
- 6ZCA
- Type
- protein
- Length
- 3,640 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable DNA-directed RNA polymerase subunit DELTA,PROBABLE DNA-directed RNA polymerase…
- EC
- 2.7.7.6, 3.6.4.12
- UniProt
- A0A0D1KIU7, A0A410WI33, A0A063XB83, A0A2J0WBQ0, A0A063XB23, A0A164TSE8
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 7 distinct chains · 36% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Probable DNA-directed RNA polymerase subunit DELTA,PROBABLE DNA-directed RNA polymerase subunit DELTA,PROBABLE DNA-directed RNA polymerase subunit delta | protein | 140 | 57% helix, 4% strand | A0A0D1KIU7 |
| E | RNA polymerase subunit omega | protein | 69 | 22% helix, 20% strand | A0A410WI33 |
| U | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 231 | 26% helix, 28% strand | A0A063XB83 |
| V | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 227 | 24% helix, 21% strand | A0A063XB83 |
| X | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1075 | 26% helix, 24% strand | A0A2J0WBQ0 |
| Y | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1127 | 41% helix, 10% strand | A0A063XB23 |
| H | DNA helicase (EC 3.6.4.12) | protein | 771 | 48% helix, 8% strand | A0A164TSE8 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains 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 | 835 | 0.85 | 0.88 | 115 | empty |
| 2 | 492 | 0.83 | 0.90 | 64 | empty |
| 3 | 696 | 0.82 | 0.86 | 87 | empty |
| 4 | 494 | 0.82 | 0.88 | 62 | empty |
| 5 | 1104 | 0.81 | 0.82 | 124 | empty |
Interfaces
14 interfaces between chains.
- X–Y · 5166 Ų buried · 30 hydrogen bonds · protein-protein
- Y–H · 4327 Ų buried · 38 hydrogen bonds · protein-protein
- U–V · 1867 Ų buried · 5 hydrogen bonds · protein-protein
- U–X · 1792 Ų buried · 17 hydrogen bonds · protein-protein
- D–Y · 1346 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6ZCA · Structure of the B. subtilis RNA POLYMERASE in complex with HelD (monomer) · 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 A0A0D1KIU7
- 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 6ZCA · PDBe 6ZCA · UniProt A0A0D1KIU7 · UniProt A0A410WI33 · UniProt A0A063XB83 · UniProt A0A2J0WBQ0 · UniProt A0A063XB23 · UniProt A0A164TSE8
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