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Crystal structure of SLM1-pH domain in complex with inositol-4-phosphate

Analyse Crystal structure of SLM1-pH domain in complex with inositol-4-phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4A6H
Type: protein
Length: 429 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphatidylinositol 4,5-bisphosphate-binding protein SLM1
UniProt: P40485
Ligands: I4D, PO4
Pockets: 4 · best druggability 0.63

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Phosphatidylinositol 4,5-bisphosphate-binding protein SLM1	protein	108	16% helix, 41% strand	P40485
C	Phosphatidylinositol 4,5-bisphosphate-binding protein SLM1	protein	107	17% helix, 41% strand	P40485
D	Phosphatidylinositol 4,5-bisphosphate-binding protein SLM1	protein	106	17% helix, 42% strand	P40485

Ligands and binding sites

I4D · D-myo-inositol-4-phosphate · ligand · 3 copies · chains A, B
PO4 · Phosphate ion · ion · 8 copies · chains A, C, B, D

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

Pockets

4 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	249	0.63	0.81	32	empty
2	226	0.61	0.81	29	empty
3	117	0.48	0.80	23	I4D
4	66	0.27	0.73	16	empty

Interfaces

6 interfaces between chains.

B–D · 892 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 806 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 419 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 300 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 296 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4A6H · Crystal structure of Slm1-PH domain in complex with Inositol-4- phosphate · the same entry in another collection · chain A against A, TM-score 1.00
P40485 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 4,5-bisphosphate-binding… · a predicted model of the same protein · chain C against A, TM-score 0.91

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 P40485
Elsewhere: RCSB PDB 4A6H · PDBe 4A6H · UniProt P40485

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