MolNFT v1 · #28640 · protein
Structure of the mediator MED7/MED21 subcomplex
1YKE · RNA polymerase II mediator complex protein MED7: “Structure of the mediator MED7/MED21 subcomplex”. X-ray diffraction, 4 pockets (best druggability 0.53). MolNFT v1 #28640 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1YKE
- Type
- protein
- Length
- 428 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA polymerase II mediator complex protein MED7; RNA polymerase II holoenzyme component…
- UniProt
- Q08278, P47822
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | RNA polymerase II mediator complex protein MED7 | protein | 98 | 87% helix, 0% strand | Q08278 |
| B | RNA polymerase II holoenzyme component SRB7 | protein | 119 | 78% helix, 0% strand | P47822 |
| D | RNA polymerase II holoenzyme component SRB7 | protein | 113 | 77% helix, 0% strand | P47822 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.53 | 0.80 | 25 | empty |
| 2 | 180 | 0.52 | 0.78 | 23 | empty |
| 3 | 94 | 0.48 | 0.81 | 19 | empty |
| 4 | 52 | 0.25 | 0.73 | 12 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2219 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2208 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 448 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 237 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 236 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1YKE · Structure of the mediator MED7/MED21 subcomplex · the same entry in another collection · chain A against A, TM-score 1.00
- P47822 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain D against A, TM-score 0.92
- Q08278 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain A against A, TM-score 0.82
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 Q08278
- Every structure of UniProt P47822
- Elsewhere: RCSB PDB 1YKE · PDBe 1YKE · UniProt Q08278 · UniProt P47822
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