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Crystal structure of soar domain

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

PDB: 3TEQ
Type: protein
Length: 402 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Stromal interaction molecule 1
UniProt: Q13586
Ligands: PO4
Pockets: 5 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 86% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Stromal interaction molecule 1	protein	100	87% helix, 0% strand	Q13586
B, C	Stromal interaction molecule 1	protein	101	85% helix, 0% strand	Q13586

Ligands and binding sites

PO4 · Phosphate ion · ion · 5 copies · chains A, C, D, 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	560	0.74	0.81	58	PO4
2	179	0.50	0.77	17	empty
3	121	0.41	0.75	15	empty
4	79	0.31	0.73	19	empty
5	59	0.28	0.73	17	empty

Interfaces

5 interfaces between chains.

A–C · 913 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 484 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 478 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 443 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 432 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3TEQ · Crystal structure of SOAR domain · the same entry in another collection · chain A against A, TM-score 1.00
Q13586 · AlphaFold monomer V2.0 prediction for stromal interaction molecule 1 (Q13586) · a predicted model of the same protein · chain B against A, TM-score 0.78

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 Q13586
Elsewhere: RCSB PDB 3TEQ · PDBe 3TEQ · UniProt Q13586

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