Research workbench

Head-Middle module of Mediator

Analyse Head-Middle module of Mediator in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6XP5
Type: protein
Length: 2,928 residues
Chains: 15
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 4.2
Source: Chaetomium thermophilum; Chaetomium thermophilum (strain DSM 1495 / CBS 144.50…
Molecule: Mediator of RNA polymerase II transcription subunit 21; Mediator of RNA polymerase II…
UniProt: G0S8E0, G0S7Z4, G0SGT8, G0SEM4, G0S292, G0SCL5, G0S1R5, G0S1W4, G0SCZ3, G0SH09, G0RYQ4, G0S3J8, G0SEC7
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · resolution 4.2 · 15 distinct chains · 39% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
U	Mediator of RNA polymerase II transcription subunit 21	protein	129	68% helix, 0% strand	G0S8E0
D	Mediator of RNA polymerase II transcription subunit 4	protein	134	57% helix, 0% strand	G0S7Z4
F	Mediator of RNA polymerase II transcription subunit 6	protein	156	28% helix, 12% strand	G0SGT8
G	Mediator of RNA polymerase II transcription subunit 7	protein	122	65% helix, 0% strand	G0SEM4
I	Mediator of RNA polymerase II transcription subunit 9	protein	96	55% helix, 0% strand	G0S292
N	Mediator of RNA polymerase II transcription subunit 14	protein	544	26% helix, 9% strand	G0SCL5
Q	Mediator of RNA polymerase II transcription subunit 17	protein	476	33% helix, 10% strand	G0S1R5
Z	Mediator of RNA polymerase II transcription subunit 31	protein	98	48% helix, 0% strand	G0S1W4
H	Mediator of RNA polymerase II transcription subunit 8	protein	146	63% helix, 0% strand	G0SCZ3
K	Mediator of RNA polymerase II transcription subunit 11	protein	107	58% helix, 0% strand	G0SH09
R	Mediator of RNA polymerase II transcription subunit 18	protein	207	18% helix, 23% strand	G0RYQ4
V	Med22	protein	112	63% helix, 0% strand	G0S3J8
a	Mediator of RNA polymerase II transcription subunit 1	protein	380	16% helix, 14% strand	G0SEC7
b	Unknown peptide	protein	21	86% helix, 0% strand	—
c	Heat	protein	200	58% 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	987	0.87	0.88	103	empty
2	1068	0.86	0.87	110	empty
3	1112	0.83	0.84	118	empty
4	640	0.82	0.87	66	empty
5	806	0.82	0.85	89	empty

Interfaces

36 interfaces between chains.

N–Q · 1480 Å² buried · 3 hydrogen bonds · protein-protein
K–V · 1464 Å² buried · 8 hydrogen bonds · protein-protein
F–H · 1271 Å² buried · 3 hydrogen bonds · protein-protein
Q–V · 1264 Å² buried · 1 hydrogen bond · protein-protein
U–G · 1140 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6XP5 · Head-middle module of mediator · the same entry in another collection · chain D against D, 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 G0S8E0
Every structure of UniProt G0S7Z4
Every structure of UniProt G0SGT8
Every structure of UniProt G0SEM4
Every structure of UniProt G0S292
Every structure of UniProt G0SCL5
Every structure of UniProt G0S1R5
Every structure of UniProt G0S1W4
Every structure of UniProt G0SCZ3
Every structure of UniProt G0SH09
Every structure of UniProt G0RYQ4
Every structure of UniProt G0S3J8
Every structure of UniProt G0SEC7
Elsewhere: RCSB PDB 6XP5 · PDBe 6XP5 · UniProt G0S8E0 · UniProt G0S7Z4 · UniProt G0SGT8 · UniProt G0SEM4 · UniProt G0S292 · UniProt G0SCL5 · UniProt G0S1R5 · UniProt G0S1W4 · UniProt G0SCZ3 · UniProt G0SH09 · UniProt G0RYQ4 · UniProt G0S3J8 · UniProt G0SEC7

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