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Structure of pea lectin in complex with alpha-methyl-D-glucopyranoside

Analyse Structure of pea lectin in complex with alpha-methyl-D-glucopyranoside in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1HKD
Type: protein
Length: 458 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pea lectin alpha chain; Pea lectin beta chain
UniProt: P02867
Ligands: GYP, CA, MN

Structure

x-ray diffraction · 2 distinct chains · 3% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Pea lectin alpha chain	protein	181	2% helix, 45% strand	P02867
B, D	Pea lectin beta chain	protein	48	8% helix, 63% strand	P02867

Ligands and binding sites

GYP · methyl alpha-D-glucopyranoside · ligand · 2 copies · chains A, B, C, D
CA · Calcium ion · metal · 2 copies · chains A, C
MN · Manganese (II) ion · metal · 2 copies · chains A, C

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

Interfaces

5 interfaces between chains.

A–B · 3945 Å² buried · 97 hydrogen bonds · protein-protein
C–D · 3920 Å² buried · 97 hydrogen bonds · protein-protein
A–C · 960 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 173 Å² buried · 1 hydrogen bond · protein-protein
B–C · 156 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1HKD · Structure of pea lectin in complex with alpha-methyl-D-glucopyranoside · the same entry in another collection · chain A against A, TM-score 1.00
P02867 · AlphaFold monomer V2.0 prediction for lectin (P02867) · 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 P02867
Elsewhere: RCSB PDB 1HKD · PDBe 1HKD · UniProt P02867

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