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Structure of human RIPK3-mlkl complex

Analyse Structure of human RIPK3-mlkl complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7MON
Type: protein
Length: 553 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mixed lineage kinase domain-like protein; Receptor-interacting SERINE/THREONINE-protein…
EC: 2.7.11.1
UniProt: Q8NB16, Q9Y572
Ligands: ZL1
Pockets: 5 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mixed lineage kinase domain-like protein	protein	268	41% helix, 16% strand	Q8NB16
B	Receptor-interacting SERINE/THREONINE-protein kinase 3 (EC 2.7.11.1)	protein	285	44% helix, 13% strand	Q9Y572

Ligands and binding sites

ZL1 · N-[4-({2-[(cyclopropanecarbonyl)amino]pyridin-4-yl}oxy)-3-fluorophenyl]-1-(4-fluorophenyl)-2-oxo-1,2-dihydropyridine-3-carboxamide · ligand · 2 copies · chains A, 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	601	0.70	0.78	64	ZL1
2	499	0.67	0.78	50	ZL1
3	223	0.59	0.80	31	empty
4	69	0.46	0.82	15	empty
5	79	0.33	0.74	11	empty

Interfaces

1 interface between chains.

A–B · 1178 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (phosphorylation).

Compared structures

7MON · Structure of human RIPK3-MLKL complex · the same entry in another collection · chain A against A, TM-score 1.00
Q8NB16 · AlphaFold monomer V2.0 prediction for mixed lineage kinase domain- like protein (Q8NB16) · a predicted model of the same protein · chain A against A, TM-score 0.96
Q9Y572 · AlphaFold monomer V2.0 prediction for receptor-interacting SERINE/THREONINE-protein… · a predicted model of the same protein · chain B against A, TM-score 0.94

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 Q8NB16
Every structure of UniProt Q9Y572
Elsewhere: RCSB PDB 7MON · PDBe 7MON · UniProt Q8NB16 · UniProt Q9Y572

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