MolNFT v1 · #18497 · protein
RNA polymerase II-tfiis complex
1PQV · DNA-directed RNA polymerase II largest subunit: “RNA polymerase II-tfiis complex”. X-ray diffraction, 2 ligands (ZN, MG), 12 pockets (best druggability 0.48). MolNFT v1 #18497 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1PQV
- Type
- protein
- Length
- 4,031 residues
- Chains
- 13
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase II largest subunit; DNA-directed RNA polymerase II 140 kda…
- EC
- 2.7.7.6
- UniProt
- P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P07273
- Ligands
- ZN, MG
- Pockets
- 12 · best druggability 0.48
Structure
x-ray diffraction · 13 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 | 1409 | 0% helix, 0% strand | P04050 |
| B | DNA-directed RNA polymerase II 140 kda polypeptide (EC 2.7.7.6) | protein | 1103 | 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 | DNA-directed RNA polymerase II 32 kda polypeptide (EC 2.7.7.6) | protein | 135 | 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 kda polypeptide (EC 2.7.7.6) | protein | 169 | 0% helix, 0% strand | P34087 |
| H | DNA-directed RNA polymerases I, II, and III 14.5 kda 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 kda 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 |
| S | Transcription elongation factor S-II | protein | 174 | 0% helix, 0% strand | P07273 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 200 | 0.48 | 0.73 | 54 | empty |
| 2 | 206 | 0.48 | 0.73 | 44 | empty |
| 3 | 126 | 0.41 | 0.73 | 31 | empty |
| 4 | 127 | 0.41 | 0.73 | 31 | empty |
| 5 | 111 | 0.40 | 0.74 | 27 | empty |
Interfaces
19 interfaces between chains.
- A–B · 1369 Ų buried · 0 hydrogen bonds · protein-protein
- A–E · 283 Ų buried · 0 hydrogen bonds · protein-protein
- A–F · 276 Ų buried · 0 hydrogen bonds · protein-protein
- A–S · 230 Ų buried · 0 hydrogen bonds · protein-protein
- A–H · 213 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1PQV · RNA polymerase II-TFIIS complex · the same entry in another collection · chain S against S, 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
- Every structure of UniProt P07273
- Elsewhere: RCSB PDB 1PQV · PDBe 1PQV · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20433 · UniProt P20434 · UniProt P20435 · UniProt P34087 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422 · UniProt P07273
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