7W4B

Phloem lectin (PP2) structure -complex with Chitotrise

PDB DOI: https://doi.org/10.2210/pdb7W4B/pdb

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

Deposited: 2021-11-26 Released: 2023-03-08
Deposition Author(s): Sivaji, N., Kishore, B.B., Suguna, K., Surolia, A.
Funding Organization(s): Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.302
R-Value Work: 0.287

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

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

Sivaji, N., Kishore, B.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: 218.58 kDa
Atom Count: 14,777
Modelled Residue Count: 1,752
Deposited Residue Count: 1,848
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phloem lectin	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8LK69
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M, N, O, P, Q M, N, O, P, Q, R, S, T, U, V, W	3		N/A	Interactions Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Interactions & Density Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W
Glycosylation Resources
GlyTouCan: G47362BJ GlyCosmos: G47362BJ GlyGen: G47362BJ

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.302
R-Value Work: 0.287
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.29	α = 90
b = 92.41	β = 90
c = 280.78	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: 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

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 R01GM133198.