Research workbench
Complete RNA polymerase II elongation complex III with a T-U mismatch and a frayed RNA 3'-uridine
Analyse Complete RNA polymerase II elongation complex III with a T-U mismatch and a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HOW
- Type
- protein + DNA + RNA
- Length
- 3,952 residues
- Chains
- 15
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.6
- Source
- Saccharomyces cerevisiae; SYNTHETIC CONSTRUCT
- Molecule
- DNA-directed RNA polymerase II subunit RPB1; DNA-directed RNA polymerase II subunit RPB2…
- EC
- 2.7.7.6
- UniProt
- P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · resolution 3.6 · 15 distinct chains · 31% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6) | protein | 1416 | 40% helix, 15% strand | P04050 |
| B | DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6) | protein | 1112 | 27% helix, 21% strand | P08518 |
| C | DNA-directed RNA polymerase II subunit RPB3 (EC 2.7.7.6) | protein | 266 | 23% helix, 20% strand | P16370 |
| D | DNA-directed RNA polymerase II subunit RPB4 (EC 2.7.7.6) | protein | 178 | 45% helix, 4% strand | P20433 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 (EC 2.7.7.6) | protein | 214 | 38% helix, 21% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 (EC 2.7.7.6) | protein | 87 | 30% helix, 16% strand | P20435 |
| G | DNA-directed RNA polymerase II subunit RPB7 (EC 2.7.7.6) | protein | 171 | 9% helix, 46% strand | P34087 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 (EC 2.7.7.6) | protein | 134 | 2% helix, 43% strand | P20436 |
| I | DNA-directed RNA polymerase II subunit RPB9 (EC 2.7.7.6) | protein | 114 | 0% helix, 24% strand | P27999 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 (EC 2.7.7.6) | protein | 65 | 46% helix, 2% strand | P22139 |
| K | DNA-directed RNA polymerase II subunit RPB11 (EC 2.7.7.6) | protein | 114 | 37% helix, 23% strand | P38902 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 (EC 2.7.7.6) | protein | 44 | 0% helix, 9% strand | P40422 |
| 2 | 5'-D(*AP*CP*TP*AP*CP*TP*TP*GP*AP*GP*CP*T)-3' | dna | 7 | — | — |
| 1 | 5'-D(*AP*GP*CP*TP*C*AP*AP*GP*TP*AP*GP*TP*TP*AP*TP*GP*CP*CP*(BRU)P*GP*GP*TP*CP*AP*TP*T)-3' | dna | 19 | — | — |
| 3 | 5'-R(*UP*GP*CP*AP*UP*UP*U*CP*AP*AP*CP*CP*AP*GP*GP*CP*UP*U)-3' | rna | 11 | — | — |
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 | 1121 | 0.89 | 0.90 | 125 | empty |
| 2 | 1184 | 0.87 | 0.89 | 114 | empty |
| 3 | 1020 | 0.84 | 0.85 | 79 | empty |
| 4 | 745 | 0.82 | 0.86 | 72 | empty |
| 5 | 543 | 0.80 | 0.86 | 64 | empty |
Interfaces
37 interfaces between chains.
- A–B · 9846 Ų buried · 146 hydrogen bonds · protein-protein
- D–G · 2498 Ų buried · 23 hydrogen bonds · protein-protein
- A–E · 2245 Ų buried · 28 hydrogen bonds · protein-protein
- A–F · 2156 Ų buried · 19 hydrogen bonds · protein-protein
- C–K · 2122 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3HOW · Complete RNA polymerase II elongation complex III with a T-U mismatch and a frayed RNA… · the same entry in another collection · chain G against G, 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 P04050
- Every structure of UniProt P08518
- Every structure of UniProt P16370
- Every structure of UniProt P20433
- Every structure of UniProt P20434
- Every structure of UniProt P20435
- Every structure of UniProt P34087
- Every structure of UniProt P20436
- Every structure of UniProt P27999
- Every structure of UniProt P22139
- Every structure of UniProt P38902
- Every structure of UniProt P40422
- Elsewhere: RCSB PDB 3HOW · PDBe 3HOW · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20433 · UniProt P20434 · UniProt P20435 · UniProt P34087 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422
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