5D9Z | pdb_00005d9z

Structure of Colocasia Esculenta Agglutinin with mannose bound

• PDB DOI: https://doi.org/10.2210/pdb5D9Z/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Colocasia esculenta
• Mutation(s): No 


• Deposited: 2015-08-19 Released: 2016-02-24 
• Deposition Author(s): Chattopadhyaya, R.
• Funding Organization(s): DST, Government of India

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.369 (Depositor), 0.373 (DCC) 
• R-Value Work: 
  0.316 (Depositor), 0.324 (DCC) 
• R-Value Observed: 
  0.317 (Depositor) 

Starting Model: experimental

Literature

High resolution crystal structures of Colocasia esculenta agglutinin with and without mannose

Chattopadhyaya, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 25.5 kDa 
• Atom Count: 1,814 
• Modeled Residue Count: 221 
• Deposited Residue Count: 221 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tuber agglutinin	A	109	Colocasia esculenta	Mutation(s): 0
UniProt
Find proteins for R9RL27 (Colocasia esculenta) Explore R9RL27  Go to UniProtKB:  R9RL27

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tuber agglutinin	B	112	Colocasia esculenta	Mutation(s): 0
UniProt
Find proteins for R9RL27 (Colocasia esculenta) Explore R9RL27  Go to UniProtKB:  R9RL27

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BMA	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B]	beta-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
PO4	H [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.369 (Depositor), 0.373 (DCC) 
• R-Value Work:  0.316 (Depositor), 0.324 (DCC) 
• R-Value Observed: 0.317 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.896	α = 90
b = 75.896	β = 90
c = 124.065	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-02-24 
Deposition Author(s): Chattopadhyaya, R.

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Funding Organization	Location	Grant Number
DST, Government of India	India	Institutional

Revision History  

• Version 1.0: 2016-02-24
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-10-09
  Changes: Structure summary