1WBF | pdb_00001wbf

WINGED BEAN LECTIN, SACCHARIDE FREE FORM

PDB DOI: https://doi.org/10.2210/pdb1WBF/pdb

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

Deposited: 1998-12-16 Released: 1999-12-22
Deposition Author(s): Manoj, N., Srinivas, V.R., Suguna, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.257 (Depositor)
R-Value Work:
0.197 (Depositor), 0.198 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Structure of basic winged-bean lectin and a comparison with its saccharide-bound form.

Manoj, N., Srinivas, V.R., Suguna, K.

(1999) Acta Crystallogr D Biol Crystallogr 55: 794-800

PubMed: 10089310 Search on PubMed
DOI: https://doi.org/10.1107/s090744499900044x
Primary Citation Related Structures:
1WBF

PubMed Abstract:
The crystal structure of the saccharide-free form of the basic form of winged-bean agglutinin (WBAI) has been solved by the molecular-replacement method and refined at 2.3 A resolution. The final R factor is 19.7% for all data in the resolution range 8.0-2.3 A. The asymmetric unit contains two half-dimers, each located on a crystallographic twofold axis. The structure of the saccharide-free form is compared with that of the complex of WBAI with methyl-alpha-D-galactoside. The complex is composed of two dimers in the asymmetric unit. The intersubunit interactions in the dimer are nearly identical in the two structures. The binding site of the saccharide-free structure contains three ordered water molecules at positions similar to those of the hydroxyl groups of the carbohydrate which are hydrogen bonded to the protein. Superposition of the saccharide-binding sites of the two structures shows that the major changes involve expulsion of these ordered water molecules and a shift of about 0.6 A of the main-chain atoms of the variable loop.

Organizational Affiliation

Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560 012, India.

Macromolecule Content

Total Structure Weight: 54.35 kDa
Atom Count: 3,965
Modeled Residue Count: 474
Deposited Residue Count: 484
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (AGGLUTININ)	A, B	242	Psophocarpus tetragonolobus	Mutation(s): 0
UniProt
Find proteins for O24313 (Psophocarpus tetragonolobus) Explore O24313 Go to UniProtKB: O24313
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O24313
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	C [auth A], D [auth A], G [auth B], H [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	F [auth A], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.257 (Depositor)
R-Value Work: 0.197 (Depositor), 0.198 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.159	α = 90
b = 75.161	β = 106.91
c = 95.772	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 1999-12-22

Deposition Author(s):

Manoj, N.

Srinivas, V.R.

Suguna, K.

Revision History (Full details and data files)

Version 1.0: 1999-12-22
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Structure summary
Version 1.4: 2023-08-23
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.5: 2024-12-25
Changes: Advisory, Derived calculations, Structure summary