1N47

Isolectin B4 from Vicia villosa in complex with the Tn antigen

PDB DOI: https://doi.org/10.2210/pdb1N47/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Vicia villosa
Mutation(s): No

Deposited: 2002-10-30 Released: 2003-02-25
Deposition Author(s): Babino, A., Tello, D., Rojas, A., Bay, S., Osinaga, E., Alzari, P.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.238
R-Value Work: 0.188
R-Value Observed: 0.190

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of a plant lectin in complex with the Tn antigen

Babino, A., Tello, D., Rojas, A., Bay, S., Osinaga, E., Alzari, P.M.

(2003) FEBS Lett 536: 106-110

PubMed: 12586347 Search on PubMed
DOI: https://doi.org/10.1016/s0014-5793(03)00037-1
Primary Citation of Related Structures:
1N47

PubMed Abstract:
The structure of the tetrameric Vicia villosa isolectin B4 (VVLB4) in complex with a cancer antigen, the Tn glycopeptide (GalNAc-O-Ser), was determined at 2.7 A resolution. The N-acetylgalactoside moiety of the ligand binds to the primary combining site of VVLB4 in a similar way as observed for other Gal/GalNAc-specific plant lectins. The amino acid moiety of the Tn antigen is largely exposed to the solvent and makes few contacts with the protein. The structure of the complex provides a framework to understand the differences in the strength of VVLB4 binding to different sugars and emphasizes the role of a single protein residue, Tyr127, as a structural determinant of Tn-binding specificity.

Organizational Affiliation

Departamento de Bioquimica, Facultad de Medicina, Av. Gral Flores 2125, Montevideo, Uruguay.

Macromolecule Content

Total Structure Weight: 102.81 kDa
Atom Count: 7,293
Modelled Residue Count: 932
Deposited Residue Count: 932
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isolectin B4	A, B, C, D	233	Vicia villosa	Mutation(s): 0
UniProt
Find proteins for P56625 (Vicia villosa) Explore P56625 Go to UniProtKB: P56625
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P56625
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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, F, G, H	3		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G11971MR GlyCosmos: G11971MR GlyGen: G11971MR

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A2G Query on A2G Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain X [auth D] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain X [auth D]	L [auth A], P [auth B], T [auth C], X [auth D]	2-acetamido-2-deoxy-alpha-D-galactopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-CBQIKETKSA-N		Interactions Focus chain L [auth A] Focus chain P [auth B] Focus chain T [auth C] Focus chain X [auth D]
SER Query on SER Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain W [auth D] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D]	K [auth A], O [auth B], S [auth C], W [auth D]	SERINE C₃ H₇ N O₃ MTCFGRXMJLQNBG-REOHCLBHSA-N		Interactions Focus chain K [auth A] Focus chain O [auth B] Focus chain S [auth C] Focus chain W [auth D]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain V [auth D] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D]	J [auth A], N [auth B], R [auth C], V [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain V [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain U [auth D] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D]	I [auth A], M [auth B], Q [auth C], U [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.238
R-Value Work: 0.188
R-Value Observed: 0.190
Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.51	α = 90
b = 85.51	β = 90
c = 153.65	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2003-02-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-02-25
Type: Initial release
Version 1.1: 2008-04-02
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-04-03
Changes: Data collection, Database references, Refinement description, Structure summary