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Structure of inactive kinase RIP2K(K47R)

Analyse Structure of inactive kinase RIP2K(K47R) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5NG3
Type: protein
Length: 1,110 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Receptor-interacting SERINE/THREONINE-protein kinase 2
EC: 2.7.11.1, 2.7.10.2
UniProt: O43353
Ligands: SO4
Pockets: 10 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 39% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D	Receptor-interacting SERINE/THREONINE-protein kinase 2 (EC 2.7.11.1, 2.7.10.2)	protein	279	38% helix, 18% strand	O43353
B	Receptor-interacting SERINE/THREONINE-protein kinase 2 (EC 2.7.11.1, 2.7.10.2)	protein	275	39% helix, 18% strand	O43353
A	Receptor-interacting SERINE/THREONINE-protein kinase 2 (EC 2.7.11.1, 2.7.10.2)	protein	284	39% helix, 17% strand	O43353
C	Receptor-interacting SERINE/THREONINE-protein kinase 2 (EC 2.7.11.1, 2.7.10.2)	protein	272	39% helix, 18% strand	O43353

Ligands and binding sites

SO4 · Sulfate ion · ion · 22 copies · chains D, B, A, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	841	0.79	0.82	88	SO4
2	744	0.77	0.81	70	empty
3	725	0.76	0.81	64	SO4
4	646	0.76	0.82	80	SO4
5	512	0.68	0.79	61	SO4

Interfaces

3 interfaces between chains.

B–A · 1224 Å² buried · 18 hydrogen bonds · protein-protein
D–C · 1216 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 951 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (phosphorylation).

Compared structures

5NG3 · Structure of inactive kinase RIP2K(K47R) · the same entry in another collection · chain C against C, TM-score 1.00
O43353 · AlphaFold monomer V2.0 prediction for receptor-interacting SERINE/THREONINE-protein… · a predicted model of the same protein · chain C 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 O43353
Elsewhere: RCSB PDB 5NG3 · PDBe 5NG3 · UniProt O43353

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