MolNFT v1 · #12147 · protein
Crystal structure of yeast RNA polymerase II complexed with the inhibitor alpha amanitin
1K83 · DNA-directed RNA polymerase II largest subunit: “Crystal structure of yeast RNA polymerase II complexed with the inhibitor alpha amanitin”. X-ray diffraction, 2 ligands (ZN, MN), 20 pockets (best druggability 0.89). MolNFT v1 #12147…
- 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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