Research workbench
Structure of vaccinia virus DNA-dependent RNA polymerase elongation complex
Analyse Structure of vaccinia virus DNA-dependent RNA polymerase elongation complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RID
- Type
- protein + DNA + RNA
- Length
- 3,257 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-dependent RNA polymerase subunit RPO147; DNA-dependent RNA polymerase subunit RPO132…
- EC
- 2.7.7.6
- UniProt
- B9U1I2, B9U1Q1, B9U1R2, B9U1I0, B9U1M4, B9U1K4, B9U1G3, B9U1D1
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 11 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-dependent RNA polymerase subunit RPO147 (EC 2.7.7.6) | protein | 1250 | 40% helix, 17% strand | B9U1I2 |
| B | DNA-dependent RNA polymerase subunit RPO132 (EC 2.7.7.6) | protein | 1120 | 31% helix, 24% strand | B9U1Q1 |
| C | DNA-directed RNA polymerase 35 kda subunit (EC 2.7.7.6) | protein | 303 | 35% helix, 25% strand | B9U1R2 |
| E | DNA-directed RNA polymerase subunit (EC 2.7.7.6) | protein | 184 | 21% helix, 32% strand | B9U1I0 |
| F | DNA-directed RNA polymerase 19 kda subunit (EC 2.7.7.6) | protein | 103 | 56% helix, 8% strand | B9U1M4 |
| G | DNA-dependent RNA polymerase subunit RPO18 (EC 2.7.7.6) | protein | 76 | 20% helix, 47% strand | B9U1K4 |
| J | DNA-dependent RNA polymerase subunit RPO7 (EC 2.7.7.6) | protein | 61 | 41% helix, 8% strand | B9U1G3 |
| S | DNA-directed RNA polymerase 30 kda polypeptide (EC 2.7.7.6) | protein | 126 | 42% helix, 1% strand | B9U1D1 |
| N | Non-template strand DNA | dna | 7 | — | — |
| T | Template strand DNA | dna | 18 | — | — |
| P | RNA | rna | 9 | — | — |
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 | 791 | 0.86 | 0.89 | 102 | empty |
| 2 | 371 | 0.84 | 0.93 | 46 | empty |
| 3 | 1149 | 0.84 | 0.85 | 125 | empty |
| 4 | 371 | 0.82 | 0.91 | 42 | empty |
| 5 | 750 | 0.80 | 0.84 | 72 | empty |
Interfaces
22 interfaces between chains.
- A–B · 9485 Ų buried · 127 hydrogen bonds · protein-protein
- A–S · 3231 Ų buried · 27 hydrogen bonds · protein-protein
- A–F · 2702 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 2623 Ų buried · 27 hydrogen bonds · protein-protein
- B–J · 1899 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 6RID · Structure of Vaccinia Virus DNA-dependent RNA polymerase elongation complex · 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 B9U1I2
- Every structure of UniProt B9U1Q1
- Every structure of UniProt B9U1R2
- Every structure of UniProt B9U1I0
- Every structure of UniProt B9U1M4
- Every structure of UniProt B9U1K4
- Every structure of UniProt B9U1G3
- Every structure of UniProt B9U1D1
- Elsewhere: RCSB PDB 6RID · PDBe 6RID · UniProt B9U1I2 · UniProt B9U1Q1 · UniProt B9U1R2 · UniProt B9U1I0 · UniProt B9U1M4 · UniProt B9U1K4 · UniProt B9U1G3 · UniProt B9U1D1
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