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Structure of the mediator head subcomplex MED18/20

Analyse Structure of the mediator head subcomplex MED18/20 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2HZM
Type: protein
Length: 1,717 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA polymerase II mediator complex subunit 20; RNA polymerase II mediator complex subunit…
UniProt: P34162, P32585
Ligands: PO4
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 8 distinct chains · 27% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA polymerase II mediator complex subunit 20	protein	205	28% helix, 39% strand	P34162
B	RNA polymerase II mediator complex subunit 18	protein	227	31% helix, 40% strand	P32585
C	RNA polymerase II mediator complex subunit 20	protein	195	28% helix, 42% strand	P34162
D	RNA polymerase II mediator complex subunit 18	protein	233	27% helix, 38% strand	P32585
E	RNA polymerase II mediator complex subunit 20	protein	197	26% helix, 37% strand	P34162
F	RNA polymerase II mediator complex subunit 18	protein	238	28% helix, 36% strand	P32585
G	RNA polymerase II mediator complex subunit 20	protein	196	22% helix, 37% strand	P34162
H	RNA polymerase II mediator complex subunit 18	protein	226	27% helix, 39% strand	P32585

Ligands and binding sites

PO4 · Phosphate ion · ion · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1192	0.87	0.88	147	empty
2	269	0.75	0.88	47	empty
3	226	0.75	0.89	36	empty
4	244	0.72	0.87	47	empty
5	360	0.67	0.80	31	empty

Interfaces

11 interfaces between chains.

A–B · 1788 Å² buried · 26 hydrogen bonds · protein-protein
E–F · 1651 Å² buried · 31 hydrogen bonds · protein-protein
G–H · 1647 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 1633 Å² buried · 24 hydrogen bonds · protein-protein
D–F · 749 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

2HZM · Structure of the Mediator head subcomplex Med18/20 · the same entry in another collection · chain H against H, 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 C against A, TM-score 0.97

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 P34162
Every structure of UniProt P32585
Elsewhere: RCSB PDB 2HZM · PDBe 2HZM · UniProt P34162 · UniProt P32585

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