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Crystal structure of L3MBTL2-H4K20ME1 complex

Analyse Crystal structure of L3MBTL2-H4K20ME1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3F70
Type: protein
Length: 802 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: LETHAL(3)MALIGNANT brain tumor-like 2 protein
UniProt: Q969R5
Ligands: MLZ
Pockets: 8 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 16% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	LETHAL(3)MALIGNANT brain tumor-like 2 protein	protein	392	18% helix, 32% strand	Q969R5
B	LETHAL(3)MALIGNANT brain tumor-like 2 protein	protein	410	15% helix, 31% strand	Q969R5

Ligands and binding sites

MLZ · N-methyl-lysine · ligand · 2 copies · chains A, B

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

Pockets

8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1087	0.85	0.85	108	empty
2	431	0.76	0.85	42	empty
3	55	0.43	0.82	13	MLZ
4	80	0.41	0.79	15	empty
5	51	0.36	0.79	14	MLZ

Interfaces

1 interface between chains.

A–B · 810 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

3F70 · Crystal structure of L3MBTL2-H4K20me1 complex · the same entry in another collection · chain A against A, TM-score 1.00
Q969R5 · AlphaFold monomer V2.0 prediction for LETHAL(3)MALIGNANT brain tumor- like protein 2… · a predicted model of the same protein · chain B 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 Q969R5
Elsewhere: RCSB PDB 3F70 · PDBe 3F70 · UniProt Q969R5

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