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Crystal structure of SGF29 in complex with R2AK4ME3

Analyse Crystal structure of SGF29 in complex with R2AK4ME3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3MEV
Type: protein
Length: 361 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 0.84

Structure

x-ray diffraction · 3 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	178	13% helix, 36% strand	Q96ES7
C, D	Histone H3	protein	4	0% helix, 0% strand	Q92133

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A, B
GOL · Glycerol · additive · chains B

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	674	0.84	0.88	73	empty
2	131	0.48	0.78	22	GOL
3	112	0.46	0.78	22	empty
4	81	0.40	0.79	21	empty
5	66	0.31	0.75	16	empty

Interfaces

3 interfaces between chains.

A–B · 863 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 344 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 333 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (engineered, methylation).

Compared structures

3MEV · Crystal structure of SGF29 in complex with R2AK4me3 · 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 0.98

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 3MEV · PDBe 3MEV · UniProt Q96ES7 · UniProt Q92133

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