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Quasi racemic structure of allo-THR13-shk and D-shk

Analyse Quasi racemic structure of allo-THR13-shk and D-shk in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5I5B
Type: protein
Length: 70 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Kappa-stichotoxin-SHE3A; D-shk
UniProt: P29187
Ligands: LI, SO4

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Kappa-stichotoxin-SHE3A	protein	35	40% helix, 0% strand	P29187
B	D-shk	protein	35	40% helix, 0% strand	—

Ligands and binding sites

LI · Lithium ion · metal · 4 copies · chains A, B
SO4 · Sulfate ion · ion · 4 copies · chains A, B
GOL · Glycerol · additive · chains B

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

Interfaces

1 interface between chains.

A–B · 333 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 34 d-amino, 6 disulfide, 1 modified (D-amino acid, disulfide, nonstandard).

Compared structures

5I5B · quasi racemic structure of allo-Thr13-ShK and D-ShK · the same entry in another collection · chain A against A, TM-score 1.00
P29187 · AlphaFold monomer V2.0 prediction for kappa-stichotoxin-SHE3A (P29187) · a predicted model of the same protein · chain A against A, TM-score 0.89

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 P29187
Elsewhere: RCSB PDB 5I5B · PDBe 5I5B · UniProt P29187

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