2DTW

Crystal Structure of basic winged bean lectin in complex with 2Me-O-D-Galactose

PDB DOI: https://doi.org/10.2210/pdb2DTW/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Psophocarpus tetragonolobus
Mutation(s): No

Deposited: 2006-07-18 Released: 2006-11-07
Deposition Author(s): Kulkarni, K.A., Katiyar, S., Surolia, A., Vijayan, M., Suguna, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.243
R-Value Work: 0.204
R-Value Observed: 0.204

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 111.41 kDa
Atom Count: 7,962
Modelled Residue Count: 948
Deposited Residue Count: 964
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Basic agglutinin	A, B, C, D	241	Psophocarpus tetragonolobus	Mutation(s): 0
UniProt
Find proteins for O24313 (Psophocarpus tetragonolobus) Explore O24313 Go to UniProtKB: O24313
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O24313
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose	E, G, K	3		N-Glycosylation	Interactions Focus chain E Focus chain G Focus chain K Interactions & Density Focus chain E Focus chain G Focus chain K
Glycosylation Resources
GlyTouCan: G11971MR GlyCosmos: G11971MR GlyGen: G11971MR

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	2		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose	H	3		N-Glycosylation	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G91813SF GlyCosmos: G91813SF GlyGen: G91813SF

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	I	4		N-Glycosylation	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G18638YB GlyCosmos: G18638YB GlyGen: G18638YB

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose	J	3		N-Glycosylation	Interactions Focus chain J Interactions & Density Focus chain J
Glycosylation Resources
GlyTouCan: G46874CY GlyCosmos: G46874CY GlyGen: G46874CY

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain V [auth D] MOL2 format, chain V [auth D]	V [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain V [auth D] Interactions & Density Focus chain V [auth D]
2GS Query on 2GS Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain U [auth D] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D]	L [auth A], O [auth B], R [auth C], U [auth D]	2-O-methyl-alpha-D-galactopyranose C₇ H₁₄ O₆ UMPNFVHHMOSNAC-PZRMXXKTSA-N		Interactions Focus chain L [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D] Interactions & Density Focus chain L [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain Q [auth B] SDF format, chain T [auth C] SDF format, chain X [auth D] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth C] MOL2 format, chain X [auth D]	N [auth A], Q [auth B], T [auth C], X [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain Q [auth B] Focus chain T [auth C] Focus chain X [auth D] Interactions & Density Focus chain N [auth A] Focus chain Q [auth B] Focus chain T [auth C] Focus chain X [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain M [auth A] SDF format, chain P [auth B] SDF format, chain W [auth D] MOL2 format, chain S [auth C] MOL2 format, chain M [auth A] MOL2 format, chain P [auth B] MOL2 format, chain W [auth D]	M [auth A], P [auth B], S [auth C], W [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain W [auth D] Interactions & Density Focus chain M [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain W [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.243
R-Value Work: 0.204
R-Value Observed: 0.204
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.431	α = 90
b = 91.061	β = 90
c = 73.383	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MAR345	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-11-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-11-07
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2017-10-11
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: 2023-10-25
Changes: Data collection, Database references, Refinement description, Structure summary

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2DTW

Crystal Structure of basic winged bean lectin in complex with 2Me-O-D-Galactose

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

Glycosylation Resources

Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Entity ID: 6

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)