MolNFT v1 · #63496 · protein
Structure of the mediator submodule MED7N/31
3FBI · Mediator of RNA polymerase II transcription subunit 7: “Structure of the mediator submodule MED7N/31”. X-ray diffraction, 4 pockets (best druggability 0.42). MolNFT v1 #63496 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3FBI
- Type
- protein
- Length
- 294 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mediator of RNA polymerase II transcription subunit 7; Mediator of RNA polymerase II…
- UniProt
- Q08278, P38633
- Pockets
- 4 · best druggability 0.42
Structure
x-ray diffraction · 4 distinct chains · 55% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mediator of RNA polymerase II transcription subunit 7 | protein | 58 | 48% helix, 0% strand | Q08278 |
| B | Mediator of RNA polymerase II transcription subunit 31 | protein | 92 | 62% helix, 2% strand | P38633 |
| C | Mediator of RNA polymerase II transcription subunit 7 | protein | 50 | 46% helix, 0% strand | Q08278 |
| D | Mediator of RNA polymerase II transcription subunit 31 | protein | 94 | 57% helix, 2% strand | P38633 |
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.42 | 0.77 | 16 | empty |
| 2 | 90 | 0.39 | 0.77 | 16 | empty |
| 3 | 83 | 0.39 | 0.77 | 15 | empty |
| 4 | 69 | 0.34 | 0.76 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1440 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1187 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 993 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 93 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 3FBI · Structure of the Mediator submodule Med7N/31 · the same entry in another collection · chain A against A, TM-score 1.00
- P38633 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain B against A, TM-score 0.85
- 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 0.69
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 P38633
- Elsewhere: RCSB PDB 3FBI · PDBe 3FBI · UniProt Q08278 · UniProt P38633
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