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Crystal structure of ptshl in complex with an H3K4ME3 peptide

Analyse Crystal structure of ptshl in complex with an H3K4ME3 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ZNP
Type: protein
Length: 388 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Short life family protein; 15-mer peptide from histone H3.2
UniProt: B9H0V2, P59226
Ligands: ZN
Pockets: 3 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 8% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Short life family protein	protein	185	8% helix, 39% strand	B9H0V2
B	Short life family protein	protein	186	9% helix, 37% strand	B9H0V2
P	15-mer peptide from histone H3.2	protein	8	0% helix, 13% strand	P59226
Q	15-mer peptide from histone H3.2	protein	9	0% helix, 22% strand	P59226

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B

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

Pockets

3 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	698	0.73	0.79	50	empty
2	162	0.45	0.75	22	empty
3	122	0.40	0.74	21	empty

Interfaces

5 interfaces between chains.

B–Q · 719 Å² buried · 11 hydrogen bonds · protein-protein
A–P · 663 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 547 Å² buried · 6 hydrogen bonds · protein-protein
B–P · 35 Å² buried · 0 hydrogen bonds · protein-protein
A–Q · 30 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (methylation).

Compared structures

5ZNP · Crystal structure of PtSHL in complex with an H3K4me3 peptide · the same entry in another collection · chain A against A, TM-score 1.00
P59226 · AlphaFold monomer V2.0 prediction for histone H3.2 (P59226) · a predicted model of the same protein · chain P against A, TM-score 0.53

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 B9H0V2
Every structure of UniProt P59226
Elsewhere: RCSB PDB 5ZNP · PDBe 5ZNP · UniProt B9H0V2 · UniProt P59226

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