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Crystal structure of STK4 (MST1) sarah domain

Analyse Crystal structure of STK4 (MST1) sarah domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4NR2
Type: protein
Length: 398 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SERINE/THREONINE-protein kinase 4
EC: 2.7.11.1
UniProt: Q13043
Pockets: 5 · best druggability 0.65

Structure

x-ray diffraction · 3 distinct chains · 83% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G, H	SERINE/THREONINE-protein kinase 4 (EC 2.7.11.1)	protein	51	82% helix, 0% strand	Q13043
B, F	SERINE/THREONINE-protein kinase 4 (EC 2.7.11.1)	protein	47	81% helix, 0% strand	Q13043
D	SERINE/THREONINE-protein kinase 4 (EC 2.7.11.1)	protein	49	86% helix, 0% strand	Q13043

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, E, C, D, F, G, H

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	524	0.65	0.76	48	EDO
2	96	0.58	0.86	22	EDO
3	228	0.56	0.78	32	EDO
4	212	0.52	0.77	24	empty
5	68	0.31	0.73	11	empty

Interfaces

13 interfaces between chains.

G–H · 1470 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 1466 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 1429 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 1422 Å² buried · 10 hydrogen bonds · protein-protein
A–E · 765 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

4NR2 · Crystal structure of STK4 (MST1) SARAH domain · the same entry in another collection · chain H against H, TM-score 1.00
Q13043 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase 4 (Q13043) · a predicted model of the same protein · chain D against A, TM-score 0.76

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 Q13043
Elsewhere: RCSB PDB 4NR2 · PDBe 4NR2 · UniProt Q13043

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