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Crystal structure of parasite sarcocystis muris lectin sml-2

Analyse Crystal structure of parasite sarcocystis muris lectin sml-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2YIL
Type: protein
Length: 779 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Microneme antigen L2
UniProt: P81860
Ligands: CL, SO4

Structure

x-ray diffraction · 3 distinct chains · 15% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Microneme antigen L2	protein	131	16% helix, 31% strand	P81860
B, D, F	Microneme antigen L2	protein	129	14% helix, 34% strand	P81860
E	Microneme antigen L2	protein	130	15% helix, 33% strand	P81860

Ligands and binding sites

CL · Chloride ion · ion · 7 copies · chains A, B, C, D, E, F
SO4 · Sulfate ion · ion · 3 copies · chains C, E, F
GOL · Glycerol · additive · 10 copies · chains A, B, C, D, F

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

Interfaces

4 interfaces between chains.

C–D · 2119 Å² buried · 22 hydrogen bonds · protein-protein
E–F · 2064 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 2019 Å² buried · 29 hydrogen bonds · protein-protein
A–C · 20 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 36 disulfide (disulfide).

Compared structures

2YIL · Crystal Structure of Parasite Sarcocystis muris Lectin SML-2 · the same entry in another collection · chain F against F, TM-score 1.00
P81860 · AlphaFold monomer V2.0 prediction for microneme antigen L2 (P81860) · a predicted model of the same protein · chain E against A, TM-score 0.59

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 P81860
Elsewhere: RCSB PDB 2YIL · PDBe 2YIL · UniProt P81860

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