MolNFT v1 · #122234 · protein

Srpa adhesin in complex with sialyl T antigen

5IJ3 · Platelet-binding glycoprotein: “Srpa adhesin in complex with sialyl T antigen”. X-ray diffraction, 4 ligands (A2G, GAL, SIA). MolNFT v1 #122234 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5IJ3
Type: protein
Length: 390 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Platelet-binding glycoprotein
UniProt: A3CM52
Ligands: A2G, GAL, SIA, CA

Structure

x-ray diffraction · 2 distinct chains · 12% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Platelet-binding glycoprotein	protein	197	11% helix, 36% strand	A3CM52
B	Platelet-binding glycoprotein	protein	193	12% helix, 36% strand	A3CM52

Ligands and binding sites

A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · chains A
GAL · beta-D-galactopyranose · sugar · chains A
SIA · N-acetyl-alpha-neuraminic acid · sugar · chains A
CA · Calcium ion · metal · 7 copies · chains A, B
ACT · Acetate ion · additive · 6 copies · chains A, B

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

Interfaces

1 interface between chains.

A–B · 566 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (additive adduct).

Compared structures

5IJ3 · SrpA adhesin in complex with sialyl T antigen · the same entry in another collection · chain A against A, TM-score 1.00

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 A3CM52
Elsewhere: RCSB PDB 5IJ3 · PDBe 5IJ3 · UniProt A3CM52

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