5J50 | pdb_00005j50

Structure of tetrameric jacalin complexed with Gal beta-(1,3) GalNAc-alpha-OPNP

PDB DOI: https://doi.org/10.2210/pdb5J50/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Artocarpus integer
Mutation(s): No

Deposited: 2016-04-01 Released: 2017-02-08
Deposition Author(s): Abhinav, K.V., Sharma, K., Surolia, A., Vijayan, M.
Funding Organization(s): Department of Science and Technology, Govt. of India

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.233 (Depositor), 0.230 (DCC)
R-Value Work:
0.182 (Depositor), 0.180 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structure of tetrameric jacalin complexed with Gal beta-(1,3) GalNAc-alpha-OPNP

Abhinav, K.V., Sharma, K., Surolia, A., Vijayan, M.

To be published.

Macromolecule Content

Total Structure Weight: 69.41 kDa
Atom Count: 5,143
Modeled Residue Count: 594
Deposited Residue Count: 608
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Agglutinin alpha chain	A, C, E, G	133	Artocarpus integer	Mutation(s): 0
UniProt
Find proteins for P18670 (Artocarpus integer) Explore P18670 Go to UniProtKB: P18670
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P18670
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Agglutinin beta-3 chain	B, D, F, H	19	Artocarpus integer	Mutation(s): 0
UniProt
Find proteins for P18673 (Artocarpus integer) Explore P18673 Go to UniProtKB: P18673
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P18673
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose	I, J, K, L	2		N/A	Interactions Focus chain I Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain I Focus chain J Focus chain K Focus chain L
Glycosylation Resources
GlyTouCan: G00031MO GlyCosmos: G00031MO GlyGen: G00031MO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NPO Query on NPO Download Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain Q [auth C] SDF format, chain P [auth A] SDF format, chain BA [auth G] MOL2 format, chain Y [auth E] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth A] MOL2 format, chain BA [auth G] mmCIF format, chain Y [auth E] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth A] mmCIF format, chain BA [auth G]	BA [auth G], P [auth A], Q [auth C], Y [auth E]	P-NITROPHENOL C₆ H₅ N O₃ BTJIUGUIPKRLHP-UHFFFAOYSA-N		Interactions Focus chain BA [auth G] Focus chain P [auth A] Focus chain Q [auth C] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth G] Focus chain P [auth A] Focus chain Q [auth C] Focus chain Y [auth E]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain V [auth E] MOL2 format, chain V [auth E] mmCIF format, chain V [auth E]	V [auth E]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain V [auth E] Interactions & Density Focus chain V [auth E]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain CA [auth H] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain W [auth E] SDF format, chain X [auth E] SDF format, chain Z [auth F] MOL2 format, chain AA [auth G] MOL2 format, chain CA [auth H] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain W [auth E] MOL2 format, chain X [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain AA [auth G] mmCIF format, chain CA [auth H] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain W [auth E] mmCIF format, chain X [auth E] mmCIF format, chain Z [auth F]	AA [auth G] CA [auth H] M [auth A] N [auth A] O [auth A] AA [auth G], CA [auth H], M [auth A], N [auth A], O [auth A], R [auth C], S [auth C], T [auth C], U [auth C], W [auth E], X [auth E], Z [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain CA [auth H] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth E] Focus chain X [auth E] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth G] Focus chain CA [auth H] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth E] Focus chain X [auth E] Focus chain Z [auth F]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900084 Query on PRD_900084	I, J, K, L	Thomsen-Friedenreich antigen	Oligosaccharide / Antigen		Interactions Focus chain I Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain I Focus chain J Focus chain K Focus chain L

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.233 (Depositor), 0.230 (DCC)
R-Value Work: 0.182 (Depositor), 0.180 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.53	α = 90
b = 81.65	β = 100
c = 66.89	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2017-02-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Science and Technology, Govt. of India	India	--

Revision History (Full details and data files)

Version 1.0: 2017-02-08
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: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary

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Deposit Data

Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 5J50 | pdb_00005j50

Structure of tetrameric jacalin complexed with Gal beta-(1,3) GalNAc-alpha-OPNP

Structure of tetrameric jacalin complexed with Gal beta-(1,3) GalNAc-alpha-OPNP

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

Glycosylation Resources

Entity ID: 3

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

5J50 | pdb_00005j50