Research workbench
Elongation complex of RNA polymerase II with a hepatitis delta virus- derived RNA stem loop
Analyse Elongation complex of RNA polymerase II with a hepatitis delta virus- derived… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R93
- Type
- protein + RNA
- Length
- 3,940 residues
- Chains
- 13
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'- R(*UP*GP*AP*UP*UP*CP*UP*CP*UP*AP*UP*CP*GP*GP*AP*AP*UP*C)-3'); DNA-directed RNA…
- 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 0.88
Structure
x-ray diffraction · 13 distinct chains · 29% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | RNA (5'- R(*UP*GP*AP*UP*UP*CP*UP*CP*UP*AP*UP*CP*GP*GP*AP*AP*UP*C)-3') | rna | 14 | — | — |
| A | DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6) | protein | 1422 | 36% helix, 14% strand | P04050 |
| B | DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6) | protein | 1112 | 28% helix, 20% strand | P08518 |
| C | DNA-directed RNA polymerase II subunit RPB3 (EC 2.7.7.6) | protein | 267 | 23% helix, 17% strand | P16370 |
| D | DNA-directed RNA polymerase II subunit RPB4 (EC 2.7.7.6) | protein | 178 | 46% helix, 7% strand | P20433 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 (EC 2.7.7.6) | protein | 214 | 34% helix, 19% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 (EC 2.7.7.6) | protein | 88 | 27% helix, 16% strand | P20435 |
| G | DNA-directed RNA polymerase II subunit RPB7 (EC 2.7.7.6) | protein | 171 | 11% helix, 46% strand | P34087 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 (EC 2.7.7.6) | protein | 135 | 0% helix, 33% strand | P20436 |
| I | DNA-directed RNA polymerase II subunit RPB9 (EC 2.7.7.6) | protein | 116 | 0% helix, 25% strand | P27999 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 (EC 2.7.7.6) | protein | 65 | 48% helix, 0% strand | P22139 |
| K | DNA-directed RNA polymerase II subunit RPB11 (EC 2.7.7.6) | protein | 112 | 38% helix, 23% strand | P38902 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 (EC 2.7.7.6) | protein | 46 | 0% helix, 9% strand | P40422 |
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 | 1144 | 0.88 | 0.90 | 141 | empty |
| 2 | 977 | 0.85 | 0.86 | 107 | empty |
| 3 | 894 | 0.82 | 0.84 | 118 | empty |
| 4 | 1185 | 0.81 | 0.83 | 103 | empty |
| 5 | 608 | 0.81 | 0.87 | 58 | empty |
Interfaces
32 interfaces between chains.
- A–B · 9684 Ų buried · 129 hydrogen bonds · protein-protein
- D–G · 2424 Ų buried · 25 hydrogen bonds · protein-protein
- A–E · 2242 Ų buried · 27 hydrogen bonds · protein-protein
- A–F · 2129 Ų buried · 16 hydrogen bonds · protein-protein
- C–K · 2121 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2R93 · Elongation complex of RNA polymerase II with a hepatitis delta virus-derived RNA stem loop · the same entry in another collection · chain L against L, 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 2R93 · PDBe 2R93 · 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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