Research workbench

Crystal structure of SGF29 in complex with H3R2ME2SK4ME3

Analyse Crystal structure of SGF29 in complex with H3R2ME2SK4ME3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3MEU
Type: protein
Length: 360 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Saga-associated factor 29 homolog; Histone H3
UniProt: Q96ES7, Q92133
Ligands: SO4
Pockets: 5 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 13% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Saga-associated factor 29 homolog	protein	175	14% helix, 37% strand	Q96ES7
B	Saga-associated factor 29 homolog	protein	176	13% helix, 37% strand	Q96ES7
C	Histone H3	protein	5	0% helix, 0% strand	Q92133
D	Histone H3	protein	4	0% helix, 0% strand	Q92133

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	926	0.83	0.85	89	empty
2	109	0.48	0.80	21	empty
3	83	0.41	0.78	14	empty
4	74	0.36	0.77	12	empty
5	64	0.30	0.74	15	empty

Interfaces

3 interfaces between chains.

A–B · 843 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 455 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 399 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (engineered, methylation).

Compared structures

3MEU · Crystal structure of SGF29 in complex with H3R2me2sK4me3 · the same entry in another collection · chain A against A, TM-score 1.00
Q96ES7 · AlphaFold monomer V2.0 prediction for saga-associated factor 29 (Q96ES7) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q96ES7
Every structure of UniProt Q92133
Elsewhere: RCSB PDB 3MEU · PDBe 3MEU · UniProt Q96ES7 · UniProt Q92133

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