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Crystal structure of calystegia sepium agglutinin

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

PDB: 1OUW
Type: protein
Length: 602 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lectin
UniProt: P93114
Ligands: MLT
Pockets: 4 · best druggability 0.57

Structure

x-ray diffraction · 4 distinct chains · 0% helix, 64% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lectin	protein	149	0% helix, 62% strand	P93114
B	Lectin	protein	150	0% helix, 64% strand	P93114
C	Lectin	protein	152	0% helix, 64% strand	P93114
D	Lectin	protein	151	0% helix, 64% strand	P93114

Ligands and binding sites

MLT · D-malate · ligand · 2 copies · chains B, C, D
EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C, D
IMD · Imidazole · additive · 4 copies · chains A, B

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

Pockets

4 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	260	0.57	0.78	46	empty
2	91	0.34	0.75	24	empty
3	64	0.29	0.74	19	empty
4	63	0.27	0.73	23	empty

Interfaces

3 interfaces between chains.

A–B · 1245 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 1241 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 364 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (nonstandard).

Compared structures

1OUW · Crystal structure of Calystegia sepium agglutinin · the same entry in another collection · chain B against B, TM-score 1.00
P93114 · AlphaFold monomer V2.0 prediction for jacalin-related lectin calsepa (P93114) · a predicted model of the same protein · 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 P93114
Elsewhere: RCSB PDB 1OUW · PDBe 1OUW · UniProt P93114

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