Research workbench

Structure of yeast saga dubm with SGF73 N59D mutant at 2.36 ångströms resolution

Analyse Structure of yeast saga dubm with SGF73 N59D mutant at 2.36 ångströms resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4WA6
Type: protein
Length: 1,364 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin carboxyl-terminal hydrolase 8; Transcription and mRNA export factor SUS1…
EC: 3.4.19.12
UniProt: P50102, Q6WNK7, A6ZWK1, P53165
Ligands: ZN
Pockets: 15 · best druggability 0.87

Structure

x-ray diffraction · 8 distinct chains · 45% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.4.19.12)	protein	440	36% helix, 24% strand	P50102
B	Transcription and mRNA export factor SUS1	protein	96	82% helix, 3% strand	Q6WNK7
C	Saga-associated factor 11	protein	82	55% helix, 4% strand	A6ZWK1
E	Saga-associated factor 73	protein	85	36% helix, 16% strand	P53165
D	Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.4.19.12)	protein	415	37% helix, 24% strand	P50102
F	Transcription and mRNA export factor SUS1	protein	93	84% helix, 2% strand	Q6WNK7
G	Saga-associated factor 11	protein	71	59% helix, 10% strand	A6ZWK1
H	Saga-associated factor 73	protein	82	35% helix, 15% strand	P53165

Ligands and binding sites

ZN · Zinc ion · metal · 15 copies · chains A, C, E, D, G, H

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

Pockets

15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1014	0.87	0.88	100	empty
2	1141	0.84	0.85	95	empty
3	709	0.68	0.76	64	empty
4	233	0.60	0.80	27	empty
5	172	0.51	0.78	28	empty

Interfaces

14 interfaces between chains.

A–E · 3056 Å² buried · 40 hydrogen bonds · protein-protein
D–H · 2996 Å² buried · 40 hydrogen bonds · protein-protein
A–C · 1966 Å² buried · 26 hydrogen bonds · protein-protein
F–G · 1620 Å² buried · 9 hydrogen bonds · protein-protein
D–G · 1460 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

4WA6 · Structure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angstroms resolution · the same entry in another collection · chain H against H, TM-score 1.00
P50102 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 8 (P50102) · a predicted model of the same protein · chain D against A, TM-score 0.98
Q6WNK7 · AlphaFold monomer V2.0 prediction for transcription and mRNA export factor SUS1 (Q6WNK7) · a predicted model of the same protein · chain F against A, TM-score 0.92
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 A6ZWK1
Every structure of UniProt P53165
Elsewhere: RCSB PDB 4WA6 · PDBe 4WA6 · UniProt P50102 · UniProt Q6WNK7 · UniProt A6ZWK1 · UniProt P53165

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