Research workbench

Structure of the mediator head module from S. cerevisiae

Analyse Structure of the mediator head module from S. cerevisiae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4GWP
Type: protein
Length: 1,541 residues
Chains: 7
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
Pockets: 18 · best druggability 0.82

Structure

x-ray diffraction · 7 distinct chains · 44% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mediator of RNA polymerase II transcription subunit 11	protein	112	79% helix, 0% strand	Q99278
B	Mediator of RNA polymerase II transcription subunit 17	protein	492	46% helix, 14% strand	P32569
C	Mediator of RNA polymerase II transcription subunit 8	protein	184	63% helix, 0% strand	P38304
D	Mediator of RNA polymerase II transcription subunit 22	protein	121	66% helix, 0% strand	P32570
E	Mediator of RNA polymerase II transcription subunit 18	protein	253	24% helix, 35% strand	P32585
F	Mediator of RNA polymerase II transcription subunit 20	protein	209	23% helix, 40% strand	P34162
G	Mediator of RNA polymerase II transcription subunit 6	protein	170	34% helix, 21% strand	P38782

Pockets

18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	860	0.82	0.85	123	empty
2	710	0.79	0.84	97	empty
3	717	0.79	0.83	105	empty
4	357	0.78	0.88	58	empty
5	526	0.68	0.78	65	empty

Interfaces

15 interfaces between chains.

E–F · 2001 Å² buried · 32 hydrogen bonds · protein-protein
C–E · 893 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 829 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 642 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 590 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4GWP · Structure of the Mediator Head Module from S. cerevisiae · the same entry in another collection · chain G against G, TM-score 1.00
P34162 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain F against A, TM-score 0.95
P32585 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain E against A, TM-score 0.94
P32569 · 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 0.79
P38782 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain G against A, TM-score 0.73
P38304 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain C against A, TM-score 0.68

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 4GWP · PDBe 4GWP · UniProt Q99278 · UniProt P32569 · UniProt P38304 · UniProt P32570 · UniProt P32585 · UniProt P34162 · UniProt P38782

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.