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Crystal structure of human SPLA/RYANODINE receptor domain and socs box containing 1 (SPSB1) in complex with a 20-residue vasa peptide

Analyse Crystal structure of human SPLA/RYANODINE receptor domain and socs box… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3F2O
Type: protein
Length: 440 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spry domain-containing socs box protein 1; 20-mer peptide from ATP-dependent RNA helicase…
EC: 3.6.1.-
UniProt: Q96BD6, P09052
Pockets: 1 · best druggability 0.57

Structure

x-ray diffraction · 4 distinct chains · 9% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spry domain-containing socs box protein 1	protein	203	9% helix, 42% strand	Q96BD6
B	Spry domain-containing socs box protein 1	protein	204	8% helix, 44% strand	Q96BD6
C	20-mer peptide from ATP-dependent RNA helicase vasa (EC 3.6.1.-)	protein	18	28% helix, 6% strand	P09052
D	20-mer peptide from ATP-dependent RNA helicase vasa (EC 3.6.1.-)	protein	15	0% helix, 7% strand	P09052

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	330	0.57	0.76	44	empty

Interfaces

4 interfaces between chains.

A–C · 694 Å² buried · 21 hydrogen bonds · protein-protein
B–D · 680 Å² buried · 22 hydrogen bonds · protein-protein
B–C · 315 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 272 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

3F2O · Crystal Structure of human splA/ryanodine receptor domain and SOCS box containing 1… · the same entry in another collection · chain D against D, TM-score 1.00
Q96BD6 · AlphaFold monomer V2.0 prediction for spry domain-containing socs box protein 1 (Q96BD6) · a predicted model of the same protein · chain A against A, TM-score 0.99
P09052 · AlphaFold monomer V2.0 prediction for ATP-dependent RNA helicase vasa (P09052) · a predicted model of the same protein · chain C against A, TM-score 0.35

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 Q96BD6
Every structure of UniProt P09052
Elsewhere: RCSB PDB 3F2O · PDBe 3F2O · UniProt Q96BD6 · UniProt P09052

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