Research workbench
Bacteriophage N4 RNA polymerase II elongation complex 1
Analyse Bacteriophage N4 RNA polymerase II elongation complex 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DT8
- Type
- protein + DNA + RNA
- Length
- 674 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNAP1; RNAP2; DNA (5'-D(P*AP*CP*CP*CP*AP*CP*CP*AP*AP*AP*AP*A)-3'); RNA…
- UniProt
- Q8LTE4, Q8LTE3
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNAP1 | protein | 252 | 46% helix, 12% strand | Q8LTE4 |
| B | RNAP2 | protein | 404 | 55% helix, 11% strand | Q8LTE3 |
| C | DNA (5'-D(P*AP*CP*CP*CP*AP*CP*CP*AP*AP*AP*AP*A)-3') | dna | 12 | — | — |
| D | RNA (5'-R(P*UP*GP*GP*UP*GP*G)-3') | rna | 6 | — | — |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 754 | 0.79 | 0.83 | 79 | empty |
| 2 | 585 | 0.71 | 0.80 | 53 | empty |
| 3 | 69 | 0.48 | 0.83 | 14 | empty |
| 4 | 192 | 0.48 | 0.76 | 19 | empty |
| 5 | 150 | 0.47 | 0.77 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2836 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 744 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–C · 393 Ų buried · 4 hydrogen bonds · protein-nucleic
- C–D · 318 Ų buried · 34 hydrogen bonds · nucleic-nucleic
- A–D · 287 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 6DT8 · Bacteriophage N4 RNA polymerase II elongation complex 1 · 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 Q8LTE4
- Every structure of UniProt Q8LTE3
- Elsewhere: RCSB PDB 6DT8 · PDBe 6DT8 · UniProt Q8LTE4 · UniProt Q8LTE3
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