Research workbench
Structure of a transcribing T7 RNA polymerase initiation complex
Analyse Structure of a transcribing T7 RNA polymerase initiation complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QLN
- Type
- protein + DNA + RNA
- Length
- 901 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriophage T7 RNA polymerase; DNA (5- D(P*TP*AP*AP*TP*AP*CP*GP*AP*CP*TP*CP*AP*CP*TP*A)…
- EC
- 2.7.7.6
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriophage T7 RNA polymerase (EC 2.7.7.6) | protein | 862 | 50% helix, 10% strand | — |
| N | DNA (5- D(P*TP*AP*AP*TP*AP*CP*GP*AP*CP*TP*CP*AP*CP*TP*A)-3) | dna | 14 | — | — |
| R | RNA (5- R(PPP*GP*GP*G)-3) | rna | 3 | — | — |
| T | DNA (5- D (P*CP*TP*CP*CP*CP*TP*AP*TP*AP*GP*TP*GP*AP*GP*TP*CP*GP*TP* AP*TP*TP*A)-3) | dna | 22 | — | — |
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 957 | 0.85 | 0.86 | 70 | empty |
| 2 | 1155 | 0.82 | 0.83 | 110 | empty |
| 3 | 188 | 0.53 | 0.78 | 30 | empty |
| 4 | 124 | 0.52 | 0.81 | 24 | empty |
| 5 | 264 | 0.52 | 0.75 | 43 | empty |
Interfaces
5 interfaces between chains.
- A–T · 1964 Ų buried · 47 hydrogen bonds · protein-nucleic
- A–N · 648 Ų buried · 13 hydrogen bonds · protein-nucleic
- N–T · 558 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- A–R · 382 Ų buried · 9 hydrogen bonds · protein-nucleic
- R–T · 142 Ų buried · 12 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1QLN · Structure of a transcribing T7 RNA polymerase initiation 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
- Elsewhere: RCSB PDB 1QLN · PDBe 1QLN
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