Research workbench
Structure of the complete vaccinia DNA-dependent RNA polymerase complex
Analyse Structure of the complete vaccinia DNA-dependent RNA polymerase complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RFL
- Type
- protein + RNA
- Length
- 6,257 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-dependent RNA polymerase subunit RPO132; DNA-directed RNA polymerase subunit…
- EC
- 2.7.7.6, 2.1.1.56, 3.6.1.15
- UniProt
- B9U1Q1, B9U1I0, B9U1M4, B9U1K4, Q1PIU7, B9U1G3, B9U1L2, B9U1J2, B9U1E2, B9U1M6, B9U1I2, B9U1K8, B9U1R2, B9U1D1
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 16 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA-dependent RNA polymerase subunit RPO132 (EC 2.7.7.6) | protein | 1129 | 28% helix, 23% strand | B9U1Q1 |
| E | DNA-directed RNA polymerase subunit (EC 2.7.7.6) | protein | 184 | 19% helix, 22% strand | B9U1I0 |
| F | DNA-directed RNA polymerase 19 kda subunit (EC 2.7.7.6) | protein | 103 | 54% helix, 6% strand | B9U1M4 |
| G | DNA-dependent RNA polymerase subunit RPO18 (EC 2.7.7.6) | protein | 153 | 10% helix, 53% strand | B9U1K4 |
| I | Putative H4L RNA polymerase-associated transcription factor RAP94 (EC 2.7.7.6) | protein | 773 | 42% helix, 12% strand | Q1PIU7 |
| J | DNA-dependent RNA polymerase subunit RPO7 (EC 2.7.7.6) | protein | 61 | 33% helix, 8% strand | B9U1G3 |
| L | Small subunit of mRNA capping enzyme (EC 2.1.1.56) | protein | 284 | 40% helix, 13% strand | B9U1L2 |
| O | Large subunit of mRNA capping enzyme | protein | 826 | 26% helix, 31% strand | B9U1J2 |
| R | Virion core protein | protein | 129 | 12% helix, 39% strand | B9U1E2 |
| K | Transcription factor vetf 82KDA large subunit | protein | 91 | 7% helix, 30% strand | B9U1M6 |
| U | CHR17.TRNA16-glnttg | rna | 63 | — | — |
| A | DNA-dependent RNA polymerase subunit RPO147 (EC 2.7.7.6) | protein | 1272 | 40% helix, 15% strand | B9U1I2 |
| Q | Virion core protein | protein | 124 | 12% helix, 41% strand | B9U1E2 |
| Y | Nucleoside triphosphate phosphohydrolase-I (EC 3.6.1.15) | protein | 600 | 40% helix, 20% strand | B9U1K8 |
| C | DNA-directed RNA polymerase 35 kda subunit (EC 2.7.7.6) | protein | 304 | 35% helix, 21% strand | B9U1R2 |
| S | DNA-directed RNA polymerase 30 kda polypeptide (EC 2.7.7.6) | protein | 161 | 31% helix, 1% strand | B9U1D1 |
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 | 848 | 0.87 | 0.90 | 104 | empty |
| 2 | 743 | 0.86 | 0.90 | 83 | empty |
| 3 | 1012 | 0.84 | 0.85 | 112 | empty |
| 4 | 1047 | 0.84 | 0.85 | 129 | empty |
| 5 | 754 | 0.84 | 0.87 | 108 | empty |
Interfaces
41 interfaces between chains.
- B–A · 9783 Ų buried · 124 hydrogen bonds · protein-protein
- B–I · 5826 Ų buried · 55 hydrogen bonds · protein-protein
- I–A · 4937 Ų buried · 51 hydrogen bonds · protein-protein
- A–S · 4688 Ų buried · 38 hydrogen bonds · protein-protein
- E–A · 2682 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 modified (disulfide, phosphorylation).
Compared structures
- 6RFL · Structure of the complete Vaccinia DNA-dependent RNA polymerase complex · the same entry in another collection · chain B against B, 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 B9U1Q1
- Every structure of UniProt B9U1I0
- Every structure of UniProt B9U1M4
- Every structure of UniProt B9U1K4
- Every structure of UniProt Q1PIU7
- Every structure of UniProt B9U1G3
- Every structure of UniProt B9U1L2
- Every structure of UniProt B9U1J2
- Every structure of UniProt B9U1E2
- Every structure of UniProt B9U1M6
- Every structure of UniProt B9U1I2
- Every structure of UniProt B9U1K8
- Every structure of UniProt B9U1R2
- Every structure of UniProt B9U1D1
- Elsewhere: RCSB PDB 6RFL · PDBe 6RFL · UniProt B9U1Q1 · UniProt B9U1I0 · UniProt B9U1M4 · UniProt B9U1K4 · UniProt Q1PIU7 · UniProt B9U1G3 · UniProt B9U1L2 · UniProt B9U1J2 · UniProt B9U1E2 · UniProt B9U1M6 · UniProt B9U1I2 · UniProt B9U1K8 · UniProt B9U1R2 · UniProt B9U1D1
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