Research workbench

Structure of the schizosaccharomyces pombe mediator head module

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

PDB: 4H63
Type: protein
Length: 1,136 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mediator of RNA polymerase II transcription subunit 6; Mediator of RNA polymerase II…
UniProt: Q9US45, O94646, Q9P6Q0, P87306, O14198, O14010
Pockets: 16 · best druggability 0.79

Structure

x-ray diffraction · 6 distinct chains · 49% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
F	Mediator of RNA polymerase II transcription subunit 6	protein	136	30% helix, 30% strand	Q9US45
H	Mediator of RNA polymerase II transcription subunit 8	protein	174	76% helix, 3% strand	O94646
K	Mediator of RNA polymerase II transcription subunit 11	protein	98	76% helix, 0% strand	Q9P6Q0
Q	Mediator of RNA polymerase II transcription subunit 17	protein	410	47% helix, 18% strand	P87306
R	Mediator of RNA polymerase II transcription subunit 18	protein	201	13% helix, 42% strand	O14198
V	Mediator of RNA polymerase II transcription subunit 22	protein	117	71% helix, 0% strand	O14010

Pockets

16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	428	0.79	0.86	44	empty
2	101	0.77	0.98	26	empty
3	315	0.72	0.85	40	empty
4	286	0.56	0.77	35	empty
5	77	0.50	0.83	15	empty

Interfaces

13 interfaces between chains.

Q–V · 2641 Å² buried · 29 hydrogen bonds · protein-protein
H–Q · 2459 Å² buried · 23 hydrogen bonds · protein-protein
K–Q · 2154 Å² buried · 17 hydrogen bonds · protein-protein
K–V · 2075 Å² buried · 19 hydrogen bonds · protein-protein
F–H · 2030 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

4H63 · Structure of the Schizosaccharomyces pombe Mediator head module · the same entry in another collection · chain V against V, TM-score 1.00
P87306 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain Q against A, TM-score 0.99
O14198 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain R against A, TM-score 0.95
Q9US45 · 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 0.91
O94646 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain H against A, TM-score 0.68
Q9P6Q0 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain K against A, TM-score 0.65
O14010 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain V against A, TM-score 0.65

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 Q9US45
Every structure of UniProt O94646
Every structure of UniProt Q9P6Q0
Every structure of UniProt P87306
Every structure of UniProt O14198
Every structure of UniProt O14010
Elsewhere: RCSB PDB 4H63 · PDBe 4H63 · UniProt Q9US45 · UniProt O94646 · UniProt Q9P6Q0 · UniProt P87306 · UniProt O14198 · UniProt O14010

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