4D69 | pdb_00004d69

SOYBEAN AGGLUTININ FROM GLYCINE MAX IN COMPLEX WITH THE ANTIGEN Tn

PDB DOI: https://doi.org/10.2210/pdb4D69/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Glycine max, synthetic construct
Mutation(s): No

Deposited: 2014-11-10 Released: 2014-11-19
Deposition Author(s): Madariaga, D., Martinez-Saez, N., Somovilla, V.J., Coelho, H., Valero-Gonzalez, J., Castro-Lopez, J., Asensio, J.L., Jimenez-Barbero, J., Busto, J.H., Avenoza, A., Marcelo, F., Hurtado-Guerrero, R., Corzana, F., Peregrina, J.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.274 (Depositor), 0.271 (DCC)
R-Value Work:
0.230 (Depositor), 0.233 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Detection of Tumor-Associated Glycopeptides by Lectins: The Peptide Context Modulates Carbohydrate Recognition.

Madariaga, D., Martinez-Saez, N., Somovilla, V.J., Coelho, H., Valero-Gonzalez, J., Castro-Lopez, J., Asensio, J.L., Jimenez-Barbero, J., Busto, J.H., Avenoza, A., Marcelo, F., Hurtado-Guerrero, R., Corzana, F., Peregrina, J.M.

(2015) ACS Chem Biol 10: 747

PubMed: 25457745 Search on PubMed
DOI: https://doi.org/10.1021/cb500855x
Primary Citation Related Structures:
4D69

PubMed Abstract:
Tn antigen (α-O-GalNAc-Ser/Thr) is a convenient cancer biomarker that is recognized by antibodies and lectins. This work yields remarkable results for two plant lectins in terms of epitope recognition and reveals that these receptors show higher affinity for Tn antigen when it is incorporated in the Pro-Asp-Thr-Arg (PDTR) peptide region of mucin MUC1. In contrast, a significant affinity loss is observed when Tn antigen is located in the Ala-His-Gly-Val-Thr-Ser-Ala (AHGVTSA) or Ala-Pro-Gly-Ser-Thr-Ala-Pro (APGSTAP) fragments. Our data indicate that the charged residues, Arg and Asp, present in the PDTR sequence establish noteworthy fundamental interactions with the lectin surface as well as fix the conformation of the peptide backbone, favoring the presentation of the sugar moiety toward the lectin. These results may help to better understand glycopeptide-lectin interactions and may contribute to engineer new binding sites, allowing novel glycosensors for Tn antigen detection to be designed.

Organizational Affiliation

Centro de Investigación en Síntesis Química, Departamento de Química, Universidad de La Rioja, E-26006 Logroño, Spain.

Macromolecule Content

Total Structure Weight: 346.93 kDa
Atom Count: 22,512
Modeled Residue Count: 2,822
Deposited Residue Count: 3,096
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LECTIN	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	253	Glycine max	Mutation(s): 0
UniProt
Find proteins for P05046 (Glycine max) Explore P05046 Go to UniProtKB: P05046
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05046
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SHORT ANTIGEN PEPTIDE	M [auth O] N [auth P] O [auth Q] P [auth R] Q [auth S] M [auth O], N [auth P], O [auth Q], P [auth R], Q [auth S], R [auth T], S [auth U], T [auth V], U [auth W], V [auth X], W [auth Y], X [auth Z]	5	synthetic construct	Mutation(s): 0

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], BA [auth b], CA [auth c], DA [auth d], EA [auth e], AA [auth a], BA [auth b], CA [auth c], DA [auth d], EA [auth e], FA [auth f], GA [auth g], HA [auth h], IA [auth i], JA [auth j], Y [auth M], Z [auth N]	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain Y [auth M] Focus chain Z [auth N] Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain Y [auth M] Focus chain Z [auth N]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A2G Query on A2G Download:Ideal Coordinates CCD File SDF format, chain IB [auth I] SDF format, chain NA [auth B] SDF format, chain OB [auth K] SDF format, chain QA [auth C] SDF format, chain TA [auth D] SDF format, chain WA [auth E] SDF format, chain RB [auth L] SDF format, chain LB [auth J] SDF format, chain KA [auth A] SDF format, chain FB [auth H] SDF format, chain CB [auth G] SDF format, chain BB [auth F] MOL2 format, chain IB [auth I] MOL2 format, chain NA [auth B] MOL2 format, chain OB [auth K] MOL2 format, chain QA [auth C] MOL2 format, chain TA [auth D] MOL2 format, chain WA [auth E] MOL2 format, chain RB [auth L] MOL2 format, chain LB [auth J] MOL2 format, chain KA [auth A] MOL2 format, chain FB [auth H] MOL2 format, chain CB [auth G] MOL2 format, chain BB [auth F] mmCIF format, chain IB [auth I] mmCIF format, chain NA [auth B] mmCIF format, chain OB [auth K] mmCIF format, chain QA [auth C] mmCIF format, chain TA [auth D] mmCIF format, chain WA [auth E] mmCIF format, chain RB [auth L] mmCIF format, chain LB [auth J] mmCIF format, chain KA [auth A] mmCIF format, chain FB [auth H] mmCIF format, chain CB [auth G] mmCIF format, chain BB [auth F]	BB [auth F] CB [auth G] FB [auth H] IB [auth I] KA [auth A] BB [auth F], CB [auth G], FB [auth H], IB [auth I], KA [auth A], LB [auth J], NA [auth B], OB [auth K], QA [auth C], RB [auth L], TA [auth D], WA [auth E]	2-acetamido-2-deoxy-alpha-D-galactopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-CBQIKETKSA-N		Interactions Focus chain BB [auth F] Focus chain CB [auth G] Focus chain FB [auth H] Focus chain IB [auth I] Focus chain KA [auth A] Focus chain LB [auth J] Focus chain NA [auth B] Focus chain OB [auth K] Focus chain QA [auth C] Focus chain RB [auth L] Focus chain TA [auth D] Focus chain WA [auth E] Interactions & Density Focus chain BB [auth F] Focus chain CB [auth G] Focus chain FB [auth H] Focus chain IB [auth I] Focus chain KA [auth A] Focus chain LB [auth J] Focus chain NA [auth B] Focus chain OB [auth K] Focus chain QA [auth C] Focus chain RB [auth L] Focus chain TA [auth D] Focus chain WA [auth E]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain GB [auth H] SDF format, chain JB [auth I] SDF format, chain PA [auth B] SDF format, chain UA [auth D] SDF format, chain YA [auth E] SDF format, chain ZA [auth F] SDF format, chain XA [auth E] SDF format, chain VA [auth D] SDF format, chain TB [auth L] SDF format, chain SB [auth L] SDF format, chain SA [auth C] SDF format, chain RA [auth C] SDF format, chain QB [auth K] SDF format, chain PB [auth K] SDF format, chain OA [auth B] SDF format, chain NB [auth J] SDF format, chain MB [auth J] SDF format, chain MA [auth A] SDF format, chain LA [auth A] SDF format, chain KB [auth I] SDF format, chain HB [auth H] SDF format, chain EB [auth G] SDF format, chain DB [auth G] SDF format, chain AB [auth F] MOL2 format, chain GB [auth H] MOL2 format, chain JB [auth I] MOL2 format, chain PA [auth B] MOL2 format, chain UA [auth D] MOL2 format, chain YA [auth E] MOL2 format, chain ZA [auth F] MOL2 format, chain XA [auth E] MOL2 format, chain VA [auth D] MOL2 format, chain TB [auth L] MOL2 format, chain SB [auth L] MOL2 format, chain SA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain QB [auth K] MOL2 format, chain PB [auth K] MOL2 format, chain OA [auth B] MOL2 format, chain NB [auth J] MOL2 format, chain MB [auth J] MOL2 format, chain MA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain KB [auth I] MOL2 format, chain HB [auth H] MOL2 format, chain EB [auth G] MOL2 format, chain DB [auth G] MOL2 format, chain AB [auth F] mmCIF format, chain GB [auth H] mmCIF format, chain JB [auth I] mmCIF format, chain PA [auth B] mmCIF format, chain UA [auth D] mmCIF format, chain YA [auth E] mmCIF format, chain ZA [auth F] mmCIF format, chain XA [auth E] mmCIF format, chain VA [auth D] mmCIF format, chain TB [auth L] mmCIF format, chain SB [auth L] mmCIF format, chain SA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain QB [auth K] mmCIF format, chain PB [auth K] mmCIF format, chain OA [auth B] mmCIF format, chain NB [auth J] mmCIF format, chain MB [auth J] mmCIF format, chain MA [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain KB [auth I] mmCIF format, chain HB [auth H] mmCIF format, chain EB [auth G] mmCIF format, chain DB [auth G] mmCIF format, chain AB [auth F]	AB [auth F] DB [auth G] EB [auth G] GB [auth H] HB [auth H] AB [auth F], DB [auth G], EB [auth G], GB [auth H], HB [auth H], JB [auth I], KB [auth I], LA [auth A], MA [auth A], MB [auth J], NB [auth J], OA [auth B], PA [auth B], PB [auth K], QB [auth K], RA [auth C], SA [auth C], SB [auth L], TB [auth L], UA [auth D], VA [auth D], XA [auth E], YA [auth E], ZA [auth F]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain AB [auth F] Focus chain DB [auth G] Focus chain EB [auth G] Focus chain GB [auth H] Focus chain HB [auth H] Focus chain JB [auth I] Focus chain KB [auth I] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain MB [auth J] Focus chain NB [auth J] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain PB [auth K] Focus chain QB [auth K] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain SB [auth L] Focus chain TB [auth L] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain XA [auth E] Focus chain YA [auth E] Focus chain ZA [auth F] Interactions & Density Focus chain AB [auth F] Focus chain DB [auth G] Focus chain EB [auth G] Focus chain GB [auth H] Focus chain HB [auth H] Focus chain JB [auth I] Focus chain KB [auth I] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain MB [auth J] Focus chain NB [auth J] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain PB [auth K] Focus chain QB [auth K] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain SB [auth L] Focus chain TB [auth L] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain XA [auth E] Focus chain YA [auth E] Focus chain ZA [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.274 (Depositor), 0.271 (DCC)
R-Value Work: 0.230 (Depositor), 0.233 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.232	α = 90
b = 114.232	β = 90
c = 202.893	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-11-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-11-19
Type: Initial release
Version 1.1: 2014-12-17
Changes: Database references
Version 1.2: 2015-04-15
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-11-13
Changes: Structure summary