Research workbench

Structure of yeast saga dubm with SGF73 Y57A mutant at 2.8 ångströms resolution

Analyse Structure of yeast saga dubm with SGF73 Y57A mutant at 2.8 ångströms resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4W4U
Type: protein
Length: 1,309 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin carboxyl-terminal hydrolase; Transcription and mRNA export factor SUS1…
EC: 3.4.19.12
UniProt: N1P0J5, N1P8F5, N1NXA6, P53165
Ligands: ZN
Pockets: 17 · best druggability 0.87

Structure

x-ray diffraction · 8 distinct chains · 45% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin carboxyl-terminal hydrolase (EC 3.4.19.12)	protein	438	35% helix, 24% strand	N1P0J5
B	Transcription and mRNA export factor SUS1	protein	96	83% helix, 3% strand	N1P8F5
C	Saga-associated factor 11	protein	59	58% helix, 2% strand	N1NXA6
E	Saga-associated factor 73	protein	84	33% helix, 17% strand	P53165
D	Ubiquitin carboxyl-terminal hydrolase (EC 3.4.19.12)	protein	409	36% helix, 26% strand	N1P0J5
F	Transcription and mRNA export factor SUS1	protein	94	86% helix, 3% strand	N1P8F5
G	Saga-associated factor 11	protein	47	72% helix, 2% strand	N1NXA6
H	Saga-associated factor 73	protein	82	35% helix, 17% strand	P53165

Ligands and binding sites

ZN · Zinc ion · metal · 13 copies · chains A, E, D, H

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

Pockets

17 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	1023	0.87	0.88	102	empty
2	1148	0.85	0.86	107	empty
3	801	0.71	0.77	62	empty
4	53	0.51	0.87	16	empty
5	61	0.49	0.85	16	empty

Interfaces

14 interfaces between chains.

A–E · 2988 Å² buried · 42 hydrogen bonds · protein-protein
D–H · 2971 Å² buried · 36 hydrogen bonds · protein-protein
F–G · 1593 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 1499 Å² buried · 21 hydrogen bonds · protein-protein
B–C · 1428 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4W4U · Structure of yeast SAGA DUBm with Sgf73 Y57A mutant at 2.8 angstroms resolution · the same entry in another collection · chain H against H, TM-score 1.00
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 0.90

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 N1P0J5
Every structure of UniProt N1P8F5
Every structure of UniProt N1NXA6
Every structure of UniProt P53165
Elsewhere: RCSB PDB 4W4U · PDBe 4W4U · UniProt N1P0J5 · UniProt N1P8F5 · UniProt N1NXA6 · UniProt P53165

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