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Structure of the saga UBP8(S144N)/SGF11(1-72, delta-ZNF)/SUS1/SGF73 dub module

Analyse Structure of the saga UBP8(S144N)/SGF11(1-72, delta-ZNF)/SUS1/SGF73 dub module in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4FIP
Type: protein
Length: 1,326 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin carboxyl-terminal hydrolase 8; Protein SUS1; Saga-associated factor 11…
EC: 3.4.19.12
UniProt: P50102, Q6WNK7, Q03067, P53165
Ligands: ZN
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 7 distinct chains · 41% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.4.19.12)	protein	450	35% helix, 24% strand	P50102
B, F	Protein SUS1	protein	90	79% helix, 1% strand	Q6WNK7
C	Saga-associated factor 11	protein	41	83% helix, 0% strand	Q03067
D	Saga-associated factor 73	protein	88	33% helix, 11% strand	P53165
E	Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.4.19.12)	protein	441	34% helix, 28% strand	P50102
G	Saga-associated factor 11	protein	43	79% helix, 2% strand	Q03067
H	Saga-associated factor 73	protein	83	33% helix, 13% strand	P53165

Ligands and binding sites

ZN · Zinc ion · metal · 14 copies · chains A, D, E, H

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

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1158	0.83	0.84	91	empty
2	1017	0.83	0.83	74	empty
3	122	0.68	0.90	25	empty
4	169	0.55	0.80	29	empty
5	162	0.54	0.80	26	empty

Interfaces

19 interfaces between chains.

A–E · 2144 Å² buried · 20 hydrogen bonds · protein-protein
A–H · 1725 Å² buried · 29 hydrogen bonds · protein-protein
D–E · 1701 Å² buried · 24 hydrogen bonds · protein-protein
A–D · 1677 Å² buried · 18 hydrogen bonds · protein-protein
E–H · 1544 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

4FIP · Structure of the SAGA Ubp8(S144N)/Sgf11(1-72, Delta-ZnF)/Sus1/Sgf73 DUB module · the same entry in another collection · chain H against H, TM-score 1.00
Q03067 · AlphaFold monomer V2.0 prediction for saga-associated factor 11 (Q03067) · a predicted model of the same protein · chain C against A, TM-score 0.93
Q6WNK7 · AlphaFold monomer V2.0 prediction for transcription and mRNA export factor SUS1 (Q6WNK7) · a predicted model of the same protein · chain B against A, TM-score 0.93
P53165 · AlphaFold monomer V2.0 prediction for saga-associated factor 73 (P53165) · a predicted model of the same protein · chain H against A, TM-score 0.89

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 P50102
Every structure of UniProt Q6WNK7
Every structure of UniProt Q03067
Every structure of UniProt P53165
Elsewhere: RCSB PDB 4FIP · PDBe 4FIP · UniProt P50102 · UniProt Q6WNK7 · UniProt Q03067 · UniProt P53165

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