Research workbench
Orientation of RNA polymerase II within the human VP16-mediator-pol II-tfiif assembly
Analyse Orientation of RNA polymerase II within the human VP16-mediator-pol II-tfiif… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3J0K
- Type
- protein
- Length
- 3,927 residues
- Chains
- 12
- Method
- electron microscopy
- 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
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 12 distinct chains · 30% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6) | protein | 1426 | 37% helix, 13% strand | — |
| B | DNA-directed RNA polymerase II 140 kda polypeptide (EC 2.7.7.6) | protein | 1112 | 27% helix, 19% strand | — |
| C | DNA-directed RNA polymerase II 45 kda polypeptide (EC 2.7.7.6) | protein | 266 | 24% helix, 18% strand | — |
| D | DNA-directed RNA polymerase II 32 kda polypeptide (EC 2.7.7.6) | protein | 177 | 47% helix, 3% strand | — |
| E | DNA-directed RNA polymerases I, II, and III 27 kda polypeptide (EC 2.7.7.6) | protein | 214 | 37% helix, 17% strand | — |
| F | DNA-directed RNA polymerases I, II, and III 23 kda polypeptide (EC 2.7.7.6) | protein | 84 | 31% helix, 15% strand | — |
| G | DNA-directed RNA polymerase II 19 kda polypeptide (EC 2.7.7.6) | protein | 171 | 9% helix, 49% strand | — |
| H | DNA-directed RNA polymerases I, II, and III 14.5 kda polypeptide (EC 2.7.7.6) | protein | 133 | 2% helix, 43% strand | — |
| I | DNA-directed RNA polymerase II subunit 9 (EC 2.7.7.6) | protein | 119 | 0% helix, 10% strand | — |
| J | DNA-directed RNA polymerases I/II/III subunit 10 (EC 2.7.7.6) | protein | 65 | 49% helix, 0% strand | — |
| K | DNA-directed RNA polymerase II 13.6 kda polypeptide (EC 2.7.7.6) | protein | 114 | 38% helix, 22% strand | — |
| L | DNA-directed RNA polymerases I, II, and III 7.7 kda polypeptide (EC 2.7.7.6) | protein | 46 | 0% helix, 11% strand | — |
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 | 643 | 0.86 | 0.90 | 84 | empty |
| 2 | 1033 | 0.85 | 0.86 | 101 | empty |
| 3 | 430 | 0.83 | 0.90 | 53 | empty |
| 4 | 487 | 0.80 | 0.87 | 75 | empty |
| 5 | 538 | 0.79 | 0.85 | 58 | empty |
Interfaces
29 interfaces between chains.
- A–B · 9883 Ų buried · 131 hydrogen bonds · protein-protein
- D–G · 2244 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 2152 Ų buried · 22 hydrogen bonds · protein-protein
- C–K · 2129 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 2087 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3J0K · Orientation of RNA polymerase II within the human VP16-Mediator-pol II-TFIIF assembly · 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
- Elsewhere: RCSB PDB 3J0K · PDBe 3J0K
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