6TT9

rTBL Recombinant Lectin From Tepary Bean

• PDB DOI: https://doi.org/10.2210/pdb6TT9/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Phaseolus acutifolius
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2019-12-26 Released: 2020-05-13 
• Deposition Author(s): Martinez Alarcon, D., Varrot, A.
• Funding Organization(s): Consejo Nacional de Ciencia y Tecnologia (CONACYT), European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.213 
• R-Value Work: 0.169 

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 114.16 kDa 
• Atom Count: 7,916 
• Modelled Residue Count: 924 
• Deposited Residue Count: 1,020 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phytohemagglutinin	A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	255	Phaseolus acutifolius	Mutation(s): 0
UniProt
Find proteins for Q40750 (Phaseolus acutifolius) Explore Q40750  Go to UniProtKB:  Q40750

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth A]	8		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G61846BY GlyCosmos:  G61846BY GlyGen:  G61846BY

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth B], G [auth C]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth D]	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G02763QD GlyCosmos:  G02763QD GlyGen:  G02763QD

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEX	K [auth AAA], N [auth BBB], Q [auth CCC], R [auth CCC], U [auth DDD]	HEXANE C6 H14 VLKZOEOYAKHREP-UHFFFAOYSA-N
MN	J [auth AAA], M [auth BBB], P [auth CCC], T [auth DDD]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	I [auth AAA], L [auth BBB], O [auth CCC], S [auth DDD]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.213 
• R-Value Work: 0.169 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.572	α = 96.352
b = 64.472	β = 101.952
c = 67.59	γ = 97.268

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-05-13 
Deposition Author(s): Martinez Alarcon, D., Varrot, A.

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Funding Organization	Location	Grant Number
Consejo Nacional de Ciencia y Tecnologia (CONACYT)	Mexico	CB-2014-01-241181
European Commission	France	765581

Revision History  

• Version 1.0: 2020-05-13
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary