Research workbench
Architecture of the mediator head module
Analyse Architecture of the mediator head module in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RJ1
- Type
- protein
- Length
- 3,594 residues
- Chains
- 21
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mediator of RNA polymerase II transcription subunit 11; Mediator of RNA polymerase II…
- UniProt
- Q99278, P32569, P38304, P32570, P32585, P34162, P38782
- Ligands
- SE
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 7 distinct chains · 32% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H, O | Mediator of RNA polymerase II transcription subunit 11 | protein | 94 | 47% helix, 0% strand | Q99278 |
| B, I, P | Mediator of RNA polymerase II transcription subunit 17 | protein | 318 | 42% helix, 1% strand | P32569 |
| C, J, Q | Mediator of RNA polymerase II transcription subunit 8 | protein | 159 | 43% helix, 0% strand | P38304 |
| D, K, R | Mediator of RNA polymerase II transcription subunit 22 | protein | 88 | 52% helix, 0% strand | P32570 |
| E, L, S | Mediator of RNA polymerase II transcription subunit 18 | protein | 231 | 14% helix, 24% strand | P32585 |
| F, M, T | Mediator of RNA polymerase II transcription subunit 20 | protein | 205 | 12% helix, 26% strand | P34162 |
| G, N, U | Mediator of RNA polymerase II transcription subunit 6 | protein | 103 | 30% helix, 0% strand | P38782 |
Ligands and binding sites
- SE · Selenium atom · ion · 98 copies · chains A, B, G, D, C, E, H, I, K, J, N, L, M, O, P, U, Q, R, S, T
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 | 935 | 0.75 | 0.78 | 86 | SE |
| 2 | 994 | 0.75 | 0.78 | 92 | SE |
| 3 | 1041 | 0.74 | 0.77 | 104 | SE |
| 4 | 1045 | 0.74 | 0.77 | 98 | SE |
| 5 | 893 | 0.74 | 0.78 | 84 | SE |
Interfaces
37 interfaces between chains.
- S–T · 700 Ų buried · 6 hydrogen bonds · protein-protein
- L–M · 698 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 697 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 395 Ų buried · 0 hydrogen bonds · protein-protein
- I–J · 392 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 99 modified (engineered).
Compared structures
- 3RJ1 · Architecture of the Mediator Head module · the same entry in another collection · chain K against K, 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 Q99278
- Every structure of UniProt P32569
- Every structure of UniProt P38304
- Every structure of UniProt P32570
- Every structure of UniProt P32585
- Every structure of UniProt P34162
- Every structure of UniProt P38782
- Elsewhere: RCSB PDB 3RJ1 · PDBe 3RJ1 · UniProt Q99278 · UniProt P32569 · UniProt P38304 · UniProt P32570 · UniProt P32585 · UniProt P34162 · UniProt P38782
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