5D5G | pdb_00005d5g

Structure of colocasia esculenta agglutinin

PDB DOI: https://doi.org/10.2210/pdb5D5G/pdb

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

Deposited: 2015-08-10 Released: 2015-09-02
Deposition Author(s): Biswas, H., Chattopadhyaya, R.
Funding Organization(s): Department of Science and Technology

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free:
0.427 (Depositor), 0.430 (DCC)
R-Value Work:
0.344 (Depositor), 0.347 (DCC)
R-Value Observed:
0.345 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure Colocasia esculenta tuber agglutinin at 1.74A resolution and its quaternary interactions

Chattopadhyaya, R., Biswas, H., Sarkar, A.

(2017) J Glycobiol 6: 1000126-1000126

DOI: https://doi.org/10.4172/2168-958X.1000126

Macromolecule Content

Total Structure Weight: 49.32 kDa
Atom Count: 3,577
Modeled Residue Count: 439
Deposited Residue Count: 440
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tuber agglutinin	A, C	109	Colocasia esculenta	Mutation(s): 0
UniProt
Find proteins for R9RL27 (Colocasia esculenta) Explore R9RL27 Go to UniProtKB: R9RL27
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	R9RL27
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tuber agglutinin	B, D	111	Colocasia esculenta	Mutation(s): 0
UniProt
Find proteins for R9RL27 (Colocasia esculenta) Explore R9RL27 Go to UniProtKB: R9RL27
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	R9RL27
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	E [auth A], G [auth A], I [auth B], J [auth B], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.427 (Depositor), 0.430 (DCC)
R-Value Work: 0.344 (Depositor), 0.347 (DCC)
R-Value Observed: 0.345 (Depositor)

Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.012	α = 90
b = 47.198	β = 90
c = 82.251	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2015-09-02

Deposition Author(s):

Biswas, H.

Chattopadhyaya, R.

Funding Organization	Location	Grant Number
Department of Science and Technology	India	none

Revision History (Full details and data files)

Version 1.0: 2015-09-02
Type: Initial release
Version 1.1: 2017-08-30
Changes: Database references
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-13
Changes: Structure summary