3DZW | pdb_00003dzw

Structure of Narcissus pseudonarcissus lectin complex with Mannobiose at 1.7 A resolution, form II

• PDB DOI: https://doi.org/10.2210/pdb3DZW/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Narcissus pseudonarcissus
• Mutation(s): No 


• Deposited: 2008-07-30 Released: 2009-08-11 
• Deposition Author(s): Rizkallah, P.J., Ozbey, S., Sauerborn, M.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.213 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.187 (Depositor) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Structure of Narcissus pseudonarcissus lectin complex with Mannobiose at 1.7 A resolution, form II

Rizkallah, P.J., Ozbey, S., Sauerborn, M.K.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 26.95 kDa 
• Atom Count: 2,263 
• Modeled Residue Count: 218 
• Deposited Residue Count: 218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Agglutinin	A, B	109	Narcissus pseudonarcissus	Mutation(s): 0
UniProt
Find proteins for C0HM45 (Narcissus pseudonarcissus) Explore C0HM45  Go to UniProtKB:  C0HM45

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose	C, D, E, F, G, H	2		N/A
Glycosylation Resources
GlyTouCan: G00891MP GlyCosmos: G00891MP GlyGen: G00891MP

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	I [auth A], J [auth A], K [auth A], L [auth B], M [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900112	C, D, E, F, G, H	3alpha-alpha-mannobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.213 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.187 (Depositor) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.003	α = 90
b = 102.011	β = 90
c = 74.366	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-11 
Deposition Author(s): Rizkallah, P.J., Ozbey, S., Sauerborn, M.K.

Revision History  

• Version 1.0: 2009-08-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-08-30
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary