MolNFT v1 · #71455 · protein

Crystal structure of SGF29 in complex with H3K4ME2

3MET · Saga-associated factor 29 homolog: “Crystal structure of SGF29 in complex with H3K4ME2”. X-ray diffraction, 2 ligands (UNX, SO4), 6 pockets (best druggability 0.82). MolNFT v1 #71455 on GenesisL1: 3D structure, binding sites and…

PDB: 3MET
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: UNX, SO4
Pockets: 6 · best druggability 0.82

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	174	14% helix, 37% strand	Q96ES7
B	Saga-associated factor 29 homolog	protein	174	11% helix, 37% strand	Q96ES7
C	Histone H3	protein	8	50% helix, 0% strand	Q92133
D	Histone H3	protein	4	0% helix, 0% strand	Q92133

Ligands and binding sites

UNX · Unknown atom or ion · ion · 3 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains B, A, C
GOL · Glycerol · additive · chains B

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

Pockets

6 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	902	0.82	0.83	78	empty
2	106	0.45	0.79	15	GOL
3	99	0.45	0.79	21	empty
4	75	0.36	0.77	18	empty
5	79	0.33	0.75	15	empty

Interfaces

3 interfaces between chains.

A–B · 685 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 495 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 325 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

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

Compared structures

3MET · Crystal structure of SGF29 in complex with H3K4me2 · the same entry in another collection · chain B against B, 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 3MET · PDBe 3MET · UniProt Q96ES7 · UniProt Q92133

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