Research workbench
Crystal structure of yeast RNA polymerase II complexed with the inhibitor alpha amanitin
Analyse Crystal structure of yeast RNA polymerase II complexed with the inhibitor alpha… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1K83
- Type
- protein
- Length
- 3,498 residues
- Chains
- 11
- 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, P85421
- Ligands
- ZN, MN
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 11 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 | 1366 | 40% helix, 16% strand | P04050 |
| B | DNA-directed RNA polymerase II 140KD polypeptide (EC 2.7.7.6) | protein | 1082 | 30% helix, 23% strand | P08518 |
| C | DNA-directed RNA polymerase II 45KD polypeptide (EC 2.7.7.6) | protein | 266 | 24% helix, 25% strand | P16370 |
| E | DNA-directed RNA polymerase II 27KD polypeptide (EC 2.7.7.6) | protein | 213 | 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 | 5% helix, 41% strand | P20436 |
| I | DNA-directed RNA polymerase II 14.2KD polypeptide (EC 2.7.7.6) | protein | 122 | 2% helix, 30% strand | P27999 |
| J | DNA-directed RNA polymerase II 8.3KD polypeptide (EC 2.7.7.6) | protein | 65 | 42% helix, 5% strand | P22139 |
| K | DNA-directed RNA polymerase II 13.6KD polypeptide (EC 2.7.7.6) | protein | 114 | 39% helix, 24% strand | P38902 |
| L | DNA-directed RNA polymerase II 7.7KD polypeptide (EC 2.7.7.6) | protein | 45 | 0% helix, 13% strand | P40422 |
| M | Alpha amanitin | protein | 8 | 0% helix, 0% strand | P85421 |
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 | 980 | 0.89 | 0.90 | 119 | empty |
| 2 | 1137 | 0.86 | 0.87 | 124 | empty |
| 3 | 895 | 0.81 | 0.83 | 88 | empty |
| 4 | 900 | 0.80 | 0.82 | 112 | empty |
| 5 | 1179 | 0.79 | 0.81 | 120 | empty |
Interfaces
25 interfaces between chains.
- A–B · 8748 Ų buried · 120 hydrogen bonds · protein-protein
- A–E · 2455 Ų buried · 24 hydrogen bonds · protein-protein
- C–K · 2114 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 2016 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1812 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard, hydroxylation, oxidation).
Compared structures
- 1K83 · Crystal Structure of Yeast RNA Polymerase II Complexed with the Inhibitor Alpha Amanitin · the same entry in another collection · chain M against M, TM-score 1.00
- P85421 · AlphaFold monomer V2.0 prediction for alpha-amanitin proprotein (P85421) · a predicted model of the same protein · chain M against A, TM-score 0.29
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
- Every structure of UniProt P85421
- Elsewhere: RCSB PDB 1K83 · PDBe 1K83 · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20434 · UniProt P20435 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422 · UniProt P85421
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