Research workbench
Complete 12-subunit RNA polymerase II
Analyse Complete 12-subunit RNA polymerase II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NT9
- Type
- protein
- Length
- 3,779 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase II largest subunit; DNA-directed polymerase II second largest…
- EC
- 2.7.7.6
- UniProt
- P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422
- Pockets
- 12 · best druggability 0.47
Structure
x-ray diffraction · 12 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6) | protein | 1383 | 0% helix, 0% strand | P04050 |
| B | DNA-directed polymerase II second largest subunit (EC 2.7.7.6) | protein | 1089 | 0% helix, 0% strand | P08518 |
| C | DNA-directed RNA polymerase II 45 kda polypeptide (EC 2.7.7.6) | protein | 266 | 0% helix, 0% strand | P16370 |
| D | Yeast DNA-directed RNA polymerase II 32 kd polypeptide (EC 2.7.7.6) | protein | 97 | 0% helix, 0% strand | P20433 |
| E | DNA-directed RNA polymerases I, II, and III 27 kda polypeptide (EC 2.7.7.6) | protein | 214 | 0% helix, 0% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III 23 kda polypeptide (EC 2.7.7.6) | protein | 84 | 0% helix, 0% strand | P20435 |
| G | DNA-directed RNA polymerase II 19 kd polypeptide (EC 2.7.7.6) | protein | 169 | 0% helix, 0% strand | P34087 |
| H | DNA-directed RNA polymerases I, II, and III 14.5 kd polypeptide (EC 2.7.7.6) | protein | 133 | 0% helix, 0% strand | P20436 |
| I | DNA-directed RNA polymerase II 14.2 kda polypeptide (EC 2.7.7.6) | protein | 119 | 0% helix, 0% strand | P27999 |
| J | DNA-directed RNA polymerases I, II, and III 8.3 kda polypeptide (EC 2.7.7.6) | protein | 65 | 0% helix, 0% strand | P22139 |
| K | DNA-directed RNA polymerase II 13.6 kd polypeptide (EC 2.7.7.6) | protein | 114 | 0% helix, 0% strand | P38902 |
| L | DNA-directed RNA polymerases I, II, and III 7.7 kda polypeptide (EC 2.7.7.6) | protein | 46 | 0% helix, 0% strand | P40422 |
Pockets
12 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 193 | 0.47 | 0.73 | 47 | empty |
| 2 | 192 | 0.46 | 0.73 | 46 | empty |
| 3 | 146 | 0.41 | 0.72 | 32 | empty |
| 4 | 136 | 0.41 | 0.72 | 35 | empty |
| 5 | 116 | 0.40 | 0.73 | 34 | empty |
Interfaces
15 interfaces between chains.
- A–B · 1359 Ų buried · 0 hydrogen bonds · protein-protein
- A–E · 294 Ų buried · 0 hydrogen bonds · protein-protein
- A–I · 269 Ų buried · 0 hydrogen bonds · protein-protein
- A–F · 244 Ų buried · 0 hydrogen bonds · protein-protein
- A–H · 213 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1NT9 · Complete 12-subunit RNA polymerase II · 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 1NT9 · PDBe 1NT9 · 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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