Research workbench

Saga dub module bound to a ubiqitinated nucleosome

Analyse Saga dub module bound to a ubiqitinated nucleosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6T9L
Type: protein + DNA
Length: 1,822 residues
Chains: 15
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.2; Histone H4; Histone H2A; Histone H2B 1.1; Histone H2B; WIDOM601 DNA…
EC: 3.4.19.12
UniProt: P84233, P62799, Q6AZJ8, P02281, F6R8G8, P50102, Q6WNK7, Q03067, P53165, P0CG48
Ligands: ZN
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 15 distinct chains · 51% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.2	protein	97	68% helix, 4% strand	P84233
B	Histone H4	protein	83	61% helix, 7% strand	P62799
C	Histone H2A	protein	103	54% helix, 6% strand	Q6AZJ8
D	Histone H2B 1.1	protein	95	74% helix, 4% strand	P02281
E	Histone H3.2	protein	96	68% helix, 3% strand	P84233
F	Histone H4	protein	78	64% helix, 6% strand	P62799
G	Histone H2A	protein	105	53% helix, 4% strand	Q6AZJ8
H	Histone H2B	protein	93	75% helix, 2% strand	F6R8G8
I	WIDOM601 DNA (145-mer)	dna	145	—	—
J	WIDOM601 DNA (145-mer)	dna	145	—	—
K	Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.4.19.12)	protein	445	31% helix, 24% strand	P50102
L	Transcription and mRNA export factor SUS1	protein	89	76% helix, 0% strand	Q6WNK7
M	Saga-associated factor 11	protein	90	47% helix, 7% strand	Q03067
N	Saga-associated factor 73	protein	82	37% helix, 9% strand	P53165
O	Polyubiquitin-C	protein	76	20% helix, 33% strand	P0CG48

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains K, M, N

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

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	558	0.83	0.89	83	empty
2	432	0.83	0.90	59	empty
3	640	0.77	0.82	73	empty
4	539	0.76	0.84	51	empty
5	463	0.73	0.83	49	empty

Interfaces

48 interfaces between chains.

I–J · 6622 Å² buried · 536 hydrogen bonds · nucleic-nucleic
K–N · 3112 Å² buried · 41 hydrogen bonds · protein-protein
A–B · 2643 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 2571 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 2536 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

6T9L · SAGA DUB module bound to a ubiqitinated nucleosome · the same entry in another collection · chain O against O, TM-score 1.00

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 P84233
Every structure of UniProt P62799
Every structure of UniProt Q6AZJ8
Every structure of UniProt P02281
Every structure of UniProt F6R8G8
Every structure of UniProt P50102
Every structure of UniProt Q6WNK7
Every structure of UniProt Q03067
Every structure of UniProt P53165
Every structure of UniProt P0CG48
Elsewhere: RCSB PDB 6T9L · PDBe 6T9L · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281 · UniProt F6R8G8 · UniProt P50102 · UniProt Q6WNK7 · UniProt Q03067 · UniProt P53165 · UniProt P0CG48

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