Research workbench
RNA polymerase II crystal form II at 2.8 a resolution
Analyse RNA polymerase II crystal form II at 2.8 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1I50
- Type
- protein
- Length
- 3,558 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, MN
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 10 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6) | protein | 1419 | 39% helix, 15% strand | P04050 |
| B | DNA-directed RNA polymerase II 140KD polypeptide (EC 2.7.7.6) | protein | 1094 | 29% helix, 23% strand | P08518 |
| C | DNA-directed RNA polymerase II 45KD polypeptide (EC 2.7.7.6) | protein | 266 | 24% helix, 27% strand | P16370 |
| E | DNA-directed RNA polymerase II 27KD polypeptide (EC 2.7.7.6) | protein | 215 | 40% helix, 23% strand | P20434 |
| F | DNA-directed RNA polymerase II 23KD polypeptide (EC 2.7.7.6) | protein | 84 | 31% helix, 15% strand | P20435 |
| H | DNA-directed RNA polymerase II 14.5KD polypeptide (EC 2.7.7.6) | protein | 133 | 8% helix, 40% strand | P20436 |
| I | DNA-directed RNA polymerase II 14.2KD polypeptide (EC 2.7.7.6) | protein | 122 | 4% helix, 30% strand | P27999 |
| J | DNA-directed RNA polymerase II 8.3KD polypeptide (EC 2.7.7.6) | protein | 65 | 43% helix, 5% 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, 11% strand | P40422 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, I, J, L
- MN · Manganese (II) ion · metal · chains A
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 | 989 | 0.88 | 0.90 | 112 | empty |
| 2 | 873 | 0.86 | 0.89 | 99 | empty |
| 3 | 733 | 0.80 | 0.84 | 72 | empty |
| 4 | 1095 | 0.80 | 0.81 | 103 | empty |
| 5 | 684 | 0.78 | 0.82 | 65 | empty |
Interfaces
22 interfaces between chains.
- A–B · 9009 Ų buried · 111 hydrogen bonds · protein-protein
- A–E · 2469 Ų buried · 24 hydrogen bonds · protein-protein
- C–K · 2126 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 2002 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1808 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 1I50 · RNA polymerase II crystal form II at 2.8 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 1I50 · PDBe 1I50 · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20434 · UniProt P20435 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422
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