1BZW | pdb_00001bzw

PEANUT LECTIN COMPLEXED WITH C-LACTOSE

• PDB DOI: https://doi.org/10.2210/pdb1BZW/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Arachis hypogaea
• Mutation(s): No 


• Deposited: 1998-11-05 Released: 1998-11-11 
• Deposition Author(s): Ravishankar, R., Surolia, A., Vijayan, M., Lim, S., Kishi, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Preferred Conformation of C-Lactose at the Free and Peanut Lectin Bound States

Ravishankar, R., Surolia, A., Vijayan, M., Lim, S., Kishi, Y.

(1998) J Am Chem Soc 120: 11297-11303

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 100.57 kDa 
• Atom Count: 7,406 
• Modeled Residue Count: 928 
• Deposited Residue Count: 928 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (PEANUT LECTIN)	A, B, C, D	232	Arachis hypogaea	Mutation(s): 0
UniProt
Find proteins for P02872 (Arachis hypogaea) Explore P02872  Go to UniProtKB:  P02872

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose	E, F, H	2		N/A
Glycosylation Resources
GlyTouCan:  G88362QR GlyCosmos:  G88362QR GlyGen:  G88362QR

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	G	2		N/A
Glycosylation Resources
GlyTouCan:  G84224TW GlyCosmos:  G84224TW GlyGen:  G84224TW

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	J [auth A], L [auth B], N [auth C], P [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	I [auth A], K [auth B], M [auth C], O [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 2 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900008	E, F, H	alpha-lactose	Oligosaccharide / Nutrient

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900004	G	beta-lactose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.121	α = 90
b = 126.748	β = 90
c = 76.9	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
XDS	data reduction
XDS	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-11-11 
Deposition Author(s): Ravishankar, R., Surolia, A., Vijayan, M., Lim, S., Kishi, Y.

Revision History  

• Version 1.0: 1998-11-11
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-02-07
  Changes: Data collection, Database references, Structure summary
• Version 2.2: 2024-04-03
  Changes: Refinement description