1HKD | pdb_00001hkd

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

• PDB DOI: https://doi.org/10.2210/pdb1HKD/pdb

• Classification: PLANT LECTIN
• Organism(s): Lathyrus oleraceus
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.209 (Depositor) 
• R-Value Work: 
  0.163 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Structure of Pea Lectin in Complex with Alpha-Methyl-D-Glucopyranoside

Shevtsov, M.B., Tsygannik, I.N.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 51.77 kDa 
• Atom Count: 3,889 
• Modeled Residue Count: 460 
• Deposited Residue Count: 466 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEA LECTIN ALPHA CHAIN	A, C	181	Lathyrus oleraceus	Mutation(s): 0
UniProt
Find proteins for P02867 (Pisum sativum) Explore P02867  Go to UniProtKB:  P02867

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PEA LECTIN BETA CHAIN	B, D	52	Lathyrus oleraceus	Mutation(s): 0
UniProt
Find proteins for P02867 (Pisum sativum) Explore P02867  Go to UniProtKB:  P02867

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GYP	G [auth A], J [auth C]	methyl alpha-D-glucopyranoside C7 H14 O6 HOVAGTYPODGVJG-ZFYZTMLRSA-N
MN	F [auth A], I [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	E [auth A], H [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.209 (Depositor) 
• R-Value Work:  0.163 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.793	α = 90
b = 61.235	β = 90
c = 136.005	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2003-03-18
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-06-28
  Changes: Data collection
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary
• Version 1.5: 2023-12-13
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary