Research workbench
RNA polymerase II crystal form I at 3.1 a resolution
Analyse RNA polymerase II crystal form I at 3.1 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1I3Q
- Type
- protein
- Length
- 3,542 residues
- Chains
- 10
- 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 140KD…
- EC
- 2.7.7.6
- UniProt
- P04050, P08518, P16370, P20434, P20435, P20436, P27999, P22139, P38902, P40422
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 10 distinct chains · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6) | protein | 1414 | 39% helix, 15% strand | P04050 |
| B | DNA-directed RNA polymerase II 140KD polypeptide (EC 2.7.7.6) | protein | 1083 | 28% helix, 23% strand | P08518 |
| C | DNA-directed RNA polymerase II 45KD polypeptide (EC 2.7.7.6) | protein | 266 | 27% helix, 25% strand | P16370 |
| E | DNA-directed RNA polymerase II 27KD polypeptide (EC 2.7.7.6) | protein | 215 | 40% helix, 19% strand | P20434 |
| F | DNA-directed RNA polymerase II 23KD polypeptide (EC 2.7.7.6) | protein | 84 | 31% helix, 14% strand | P20435 |
| H | DNA-directed RNA polymerase II 14.5KD polypeptide (EC 2.7.7.6) | protein | 133 | 5% helix, 43% strand | P20436 |
| I | DNA-directed RNA polymerase II 14.2KD polypeptide (EC 2.7.7.6) | protein | 122 | 2% helix, 26% strand | P27999 |
| J | DNA-directed RNA polymerase II 8.3KD polypeptide (EC 2.7.7.6) | protein | 65 | 42% helix, 2% strand | P22139 |
| K | DNA-directed RNA polymerase II 13.6KD polypeptide (EC 2.7.7.6) | protein | 114 | 38% helix, 24% strand | P38902 |
| L | DNA-directed RNA polymerase II 7.7KD polypeptide (EC 2.7.7.6) | protein | 46 | 0% helix, 13% 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 | 983 | 0.89 | 0.90 | 130 | empty |
| 2 | 1196 | 0.86 | 0.87 | 103 | empty |
| 3 | 1065 | 0.85 | 0.86 | 158 | empty |
| 4 | 413 | 0.81 | 0.90 | 60 | empty |
| 5 | 1126 | 0.81 | 0.83 | 105 | empty |
Interfaces
23 interfaces between chains.
- A–B · 9206 Ų buried · 126 hydrogen bonds · protein-protein
- A–E · 2144 Ų buried · 25 hydrogen bonds · protein-protein
- C–K · 2097 Ų buried · 16 hydrogen bonds · protein-protein
- A–F · 1919 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1817 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 1I3Q · RNA polymerase II crystal form I at 3.1 a resolution · 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
- Every structure of UniProt P04050
- Every structure of UniProt P08518
- Every structure of UniProt P16370
- Every structure of UniProt P20434
- Every structure of UniProt P20435
- 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 1I3Q · PDBe 1I3Q · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20434 · UniProt P20435 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422
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