1HKD

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.209
  • R-Value Work: 0.163

Literature

Macromolecules
Sequence Display for 1HKD

Classification: PLANT LECTIN

Total Structure Weight: 51772.72

Macromolecule Entities
Molecule Chains Length Organism Details
PEA LECTIN ALPHA CHAIN A, C 181 Pisum sativum Fragment: RESIDUES 31-211
Details: ALPHA-METHYL-D-GLUCOPYRANOSIDE IS PRESENT IN TWO BINDING SITES OF MOLECULE
Gene Name(s): LECA PSL1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PEA LECTIN BETA CHAIN B, D 52 Pisum sativum Fragment: RESIDUES 218-269
Details: ALPHA-METHYL-D-GLUCOPYRANOSIDE IS PRESENT IN TWO BINDING SITES OF MOLECULE
Gene Name(s): LECA PSL1

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GYP
Query on GYP

A, C METHYL-ALPHA-D-GLUCOPYRANOSIDE
ALPHA-METHYL-D-GLUCOPYRANOSIDE (Synonym)
C7 H14 O6
HOVAGTYPODGVJG-ZFYZTMLRSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A, C MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, C CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.209
  • R-Value Work: 0.163
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 50.79 α = 90.00
b = 61.24 β = 90.00
c = 136.01 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-03-06
  • Released Date: 2003-03-18
  • Deposition author(s): Shevtsov, M.B., Tsygannik, I.N.

Revision History

  • 2011-05-08
    Type: Version format compliance
  • 2011-07-13
    Type: Version format compliance
  • 2017-06-28
    Type: Data collection