MolNFT v1 · #162759 · protein + DNA + RNA
Structure of vaccinia virus DNA-dependent RNA polymerase co- transcriptional capping complex
6RIE · DNA-dependent RNA polymerase subunit RPO147: “Structure of vaccinia virus DNA-dependent RNA polymerase co- transcriptional capping complex”. Electron microscopy, 3 ligands (SAM, ZN, MG), 20 pockets (best druggability 0.85). MolNFT…
- PDB
- 6RIE
- Type
- protein + DNA + RNA
- Length
- 4,459 residues
- Chains
- 13
- 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, 2.1.1.56
- UniProt
- Q1PIV1, B9U1Q1, B9U1R2, B9U1I0, B9U1M4, B9U1K4, B9U1G3, B9U1L2, B9U1J2, B9U1D1
- Ligands
- SAM, ZN, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 13 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-dependent RNA polymerase subunit RPO147 | protein | 1285 | 38% helix, 17% strand | Q1PIV1 |
| B | DNA-dependent RNA polymerase subunit RPO132 (EC 2.7.7.6) | protein | 1129 | 29% helix, 24% strand | B9U1Q1 |
| C | DNA-directed RNA polymerase 35 kda subunit (EC 2.7.7.6) | protein | 303 | 34% helix, 25% strand | B9U1R2 |
| E | DNA-directed RNA polymerase subunit (EC 2.7.7.6) | protein | 184 | 19% helix, 32% strand | B9U1I0 |
| F | DNA-directed RNA polymerase 19 kda subunit (EC 2.7.7.6) | protein | 103 | 57% helix, 8% strand | B9U1M4 |
| G | DNA-dependent RNA polymerase subunit RPO18 (EC 2.7.7.6) | protein | 131 | 12% helix, 53% strand | B9U1K4 |
| J | DNA-dependent RNA polymerase subunit RPO7 (EC 2.7.7.6) | protein | 61 | 36% helix, 8% strand | B9U1G3 |
| L | Small subunit of mRNA capping enzyme (EC 2.1.1.56) | protein | 287 | 39% helix, 15% strand | B9U1L2 |
| N | Non-template DNA strand | dna | 7 | — | — |
| O | Large subunit of mRNA capping enzyme | protein | 822 | 26% helix, 33% strand | B9U1J2 |
| P | RNA | rna | 16 | — | — |
| S | DNA-directed RNA polymerase 30 kda polypeptide (EC 2.7.7.6) | protein | 113 | 41% helix, 1% strand | B9U1D1 |
| T | Template strand DNA | dna | 18 | — | — |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains O
- ZN · Zinc ion · metal · 4 copies · chains A, B, J
- MG · Magnesium ion · metal · 2 copies · chains A, P, O
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 | 1146 | 0.85 | 0.86 | 125 | empty |
| 2 | 529 | 0.84 | 0.90 | 54 | SAM |
| 3 | 362 | 0.84 | 0.93 | 41 | empty |
| 4 | 436 | 0.83 | 0.90 | 54 | empty |
| 5 | 774 | 0.82 | 0.85 | 89 | empty |
Interfaces
29 interfaces between chains.
- A–B · 9805 Ų buried · 119 hydrogen bonds · protein-protein
- A–S · 3187 Ų buried · 28 hydrogen bonds · protein-protein
- A–F · 2884 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 2669 Ų buried · 27 hydrogen bonds · protein-protein
- B–J · 1927 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6RIE · Structure of Vaccinia Virus DNA-dependent RNA polymerase co-transcriptional capping… · 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 Q1PIV1
- 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 B9U1L2
- Every structure of UniProt B9U1J2
- Every structure of UniProt B9U1D1
- Elsewhere: RCSB PDB 6RIE · PDBe 6RIE · UniProt Q1PIV1 · UniProt B9U1Q1 · UniProt B9U1R2 · UniProt B9U1I0 · UniProt B9U1M4 · UniProt B9U1K4 · UniProt B9U1G3 · UniProt B9U1L2 · UniProt B9U1J2 · UniProt B9U1D1
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