1BQP | pdb_00001bqp

THE STRUCTURE OF THE PEA LECTIN-D-MANNOPYRANOSE COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1BQP/pdb

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


• Deposited: 1998-08-17 Released: 1998-08-26 
• Deposition Author(s): Ruzeinikov, S.N., Mikhailova, I.Y., Tsygannik, I.N., Pangborn, W., Duax, W., Pletnev, V.Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.188 (Depositor) 
• R-Value Work: 
  0.161 (Depositor) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

The Structure of the Pea Lectin-D-Mannopyranose Complex at a 2.1 A Resolution

Ruzheinikov, S.N., Mikhailova, I.Y., Tsygannik, I.N., Pangborn, W., Duax, W., Pletnev, V.Z.

(1998) Russ J Bioorg Chem 24: 277-279

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 51.27 kDa 
• Atom Count: 3,878 
• Modeled Residue Count: 456 
• Deposited Residue Count: 456 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (LECTIN)	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
PROTEIN (LECTIN)	B, D	47	Lathyrus oleraceus	Mutation(s): 0
UniProt
Find proteins for P02867 (Pisum sativum) Explore P02867  Go to UniProtKB:  P02867

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BMA	H [auth B], K [auth C]	beta-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
MAN	G [auth B], I [auth C]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
MN	F [auth A], L [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	E [auth A], J [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.188 (Depositor) 
• R-Value Work:  0.161 (Depositor) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.926	α = 90
b = 104.083	β = 90
c = 64.837	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-08-26 
Deposition Author(s): Ruzeinikov, S.N., Mikhailova, I.Y., Tsygannik, I.N., Pangborn, W., Duax, W., Pletnev, V.Z.

Revision History  

• Version 1.0: 1998-08-26
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2016-02-17
  Changes: Non-polymer description
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.5: 2023-08-09
  Changes: Data collection, Database references, Refinement description, Structure summary