7VWB | pdb_00007vwb

Phloem lectin (PP2) structure -complex with N-Acetyllactosamine (LacNAc)

PDB DOI: https://doi.org/10.2210/pdb7VWB/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Cucumis sativus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-11-10 Released: 2023-03-08
Deposition Author(s): Sivaji, N., Bobbili, K.B., Suguna, K., Surolia, A.
Funding Organization(s): Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.248 (Depositor), 0.252 (DCC)
R-Value Work:
0.218 (Depositor), 0.224 (DCC)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Structure and interactions of the phloem lectin (phloem protein 2) Cus17 from Cucumis sativus.

Sivaji, N., Bobbili, K.B., Suguna, K., Surolia, A.

(2023) Structure 31: 1-16

DOI: https://doi.org/10.1016/j.str.2023.02.008

Macromolecule Content

Total Structure Weight: 36.13 kDa
Atom Count: 2,718
Modeled Residue Count: 300
Deposited Residue Count: 308
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
phloem lectin	A, B	154	Cucumis sativus	Mutation(s): 0 Gene Names: Lec17-7
UniProt
Find proteins for Q8LK69 (Cucumis sativus) Explore Q8LK69 Go to UniProtKB: Q8LK69
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8LK69
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose	C, D	2		N/A	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G79333MY GlyCosmos: G79333MY GlyGen: G79333MY

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900019 Query on PRD_900019	C, D	N-acetyl-alpha-lactosamine	Oligosaccharide / Glycan component		Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.248 (Depositor), 0.252 (DCC)
R-Value Work: 0.218 (Depositor), 0.224 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.69	α = 90
b = 60.39	β = 99.13
c = 82.98	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-03-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	--

Revision History (Full details and data files)

Version 1.0: 2023-03-08
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-10-30
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.