Research workbench

Cryo-EM structure of the transcriptional mediator

Analyse Cryo-EM structure of the transcriptional mediator in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5U0P
Type: protein
Length: 2,929 residues
Chains: 16
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mediator complex subunit 14; Mediator complex subunit 6; Mediator complex subunit 8…
UniProt: Q9P7Y4, Q9US45, O94646, P87306, O14198, Q10317, Q9P6Q0, O14010, O60104, O94376, Q9USH1, O13964, Q10477
Pockets: 20 · best druggability 0.80

Structure

electron microscopy · 16 distinct chains · 53% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
N	Mediator complex subunit 14	protein	520	36% helix, 9% strand	Q9P7Y4
F	Mediator complex subunit 6	protein	195	32% helix, 17% strand	Q9US45
H	Mediator complex subunit 8	protein	182	76% helix, 1% strand	O94646
Q	Mediator complex subunit 17	protein	508	50% helix, 10% strand	P87306
R	Mediator complex subunit 18	protein	207	19% helix, 29% strand	O14198
T	Mediator complex subunit 20	protein	179	20% helix, 15% strand	Q10317
K	Mediator complex subunit 11	protein	98	73% helix, 0% strand	Q9P6Q0
V	Mediator complex subunit 22	protein	118	69% helix, 1% strand	O14010
D	Mediator complex subunit 4	protein	96	82% helix, 0% strand	—
G	Mediator complex subunit 7	protein	194	65% helix, 0% strand	O60104
U	Mediator complex subunit 21	protein	122	81% helix, 0% strand	O94376
3	Mediator complex subunit 31	protein	103	51% helix, 0% strand	Q9USH1
I	Mediator complex subunit 9	protein	75	69% helix, 0% strand	O13964
2	Mediator complex subunit 27	protein	78	53% helix, 13% strand	Q10477
S	Mediator complex subunit 19	protein	122	84% helix, 0% strand	—
J	Mediator complex subunit 10	protein	132	92% helix, 0% strand	—

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	479	0.80	0.87	54	empty
2	1037	0.80	0.81	127	empty
3	741	0.78	0.82	71	empty
4	1101	0.78	0.80	120	empty
5	1021	0.77	0.79	100	empty

Interfaces

41 interfaces between chains.

Q–V · 2518 Å² buried · 20 hydrogen bonds · protein-protein
H–Q · 2110 Å² buried · 20 hydrogen bonds · protein-protein
F–Q · 2045 Å² buried · 22 hydrogen bonds · protein-protein
N–Q · 2002 Å² buried · 19 hydrogen bonds · protein-protein
Q–K · 1948 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5U0P · Cryo-EM structure of the transcriptional Mediator · the same entry in another collection · chain U against U, 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 Q9P7Y4
Every structure of UniProt Q9US45
Every structure of UniProt O94646
Every structure of UniProt P87306
Every structure of UniProt O14198
Every structure of UniProt Q10317
Every structure of UniProt Q9P6Q0
Every structure of UniProt O14010
Every structure of UniProt O60104
Every structure of UniProt O94376
Every structure of UniProt Q9USH1
Every structure of UniProt O13964
Every structure of UniProt Q10477
Elsewhere: RCSB PDB 5U0P · PDBe 5U0P · UniProt Q9P7Y4 · UniProt Q9US45 · UniProt O94646 · UniProt P87306 · UniProt O14198 · UniProt Q10317 · UniProt Q9P6Q0 · UniProt O14010 · UniProt O60104 · UniProt O94376 · UniProt Q9USH1 · UniProt O13964 · UniProt Q10477

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