Research workbench

Saga core module

Analyse Saga core module in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6T9K
Type: protein
Length: 2,426 residues
Chains: 11
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcription factor SPT20; Protein SPT3; Transcription initiation factor tfiid subunit…
UniProt: P50875, P06844, P38129, P53040, Q05027, Q12030, Q12060, Q03761, P35177, P53165
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 11 distinct chains · 43% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Transcription factor SPT20	protein	181	27% helix, 18% strand	P50875
C	Protein SPT3	protein	214	59% helix, 0% strand	P06844
D	Transcription initiation factor tfiid subunit 5	protein	566	22% helix, 28% strand	P38129
E	Transcription initiation factor tfiid subunit 6	protein	433	45% helix, 3% strand	P53040
F	Transcription initiation factor tfiid subunit 9	protein	111	56% helix, 2% strand	Q05027
G	Transcription initiation factor tfiid subunit 10	protein	140	58% helix, 1% strand	Q12030
H	Transcriptional coactivator HFI1/ADA1	protein	227	50% helix, 3% strand	Q12060
I	Transcription initiation factor tfiid subunit 12	protein	108	58% helix, 4% strand	Q03761
K	Transcriptional activator SPT7	protein	279	59% helix, 1% strand	P35177
Q	Saga-associated factor 73	protein	84	33% helix, 5% strand	P53165
U	Unassigned sequence	protein	83	45% 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	487	0.88	0.95	82	empty
2	1102	0.87	0.88	92	empty
3	361	0.86	0.95	55	empty
4	615	0.84	0.89	98	empty
5	515	0.80	0.87	60	empty

Interfaces

35 interfaces between chains.

D–E · 4353 Å² buried · 54 hydrogen bonds · protein-protein
E–K · 4060 Å² buried · 36 hydrogen bonds · protein-protein
B–D · 3759 Å² buried · 36 hydrogen bonds · protein-protein
G–K · 3406 Å² buried · 22 hydrogen bonds · protein-protein
H–I · 2686 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

6T9K · SAGA Core module · the same entry in another collection · chain U against U, TM-score 1.00
P06844 · AlphaFold monomer V2.0 prediction for protein SPT3 (P06844) · a predicted model of the same protein · chain C against A, TM-score 0.94

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 P50875
Every structure of UniProt P06844
Every structure of UniProt P38129
Every structure of UniProt P53040
Every structure of UniProt Q05027
Every structure of UniProt Q12030
Every structure of UniProt Q12060
Every structure of UniProt Q03761
Every structure of UniProt P35177
Every structure of UniProt P53165
Elsewhere: RCSB PDB 6T9K · PDBe 6T9K · UniProt P50875 · UniProt P06844 · UniProt P38129 · UniProt P53040 · UniProt Q05027 · UniProt Q12030 · UniProt Q12060 · UniProt Q03761 · UniProt P35177 · UniProt P53165

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