8UX7 | pdb_00008ux7

Dioclea megacarpa lectin (DmegA) complexed with X-Man

PDB DOI: https://doi.org/10.2210/pdb8UX7/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Macropsychanthus megacarpus
Mutation(s): No

Deposited: 2023-11-09 Released: 2023-11-29
Deposition Author(s): Oliveira, M.V., De Sloover, G., Osterne, V.J.S., Pinto-Junior, V.R., Sacramento-Neto, J.C., Van Damme, E.J.M., Nascimento, K.S., Cavada, B.S.
Funding Organization(s): Coordination for the Improvement of Higher Education Personnel, Brazilian National Council for Scientific and Technological Development (CNPq), Research Foundation - Flanders (FWO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.248 (Depositor), 0.250 (DCC)
R-Value Work:
0.201 (Depositor), 0.210 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Dioclea megacarpa lectin (DmegA) complexed with X-Man

Oliveira, M.V., De Sloover, G., Osterne, V.J.S., Pinto-Junior, V.R., Sacramento-Neto, J.C., Van Damme, E.J.M., Nascimento, K.S., Cavada, B.S.

To be published.

Macromolecule Content

Total Structure Weight: 52.26 kDa
Atom Count: 3,690
Modeled Residue Count: 464
Deposited Residue Count: 474
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dioclea megacarpa lectin	A, B	237	Macropsychanthus megacarpus	Mutation(s): 0
UniProt
Find proteins for B3EWJ2 (Macropsychanthus sclerocarpus) Explore B3EWJ2 Go to UniProtKB: B3EWJ2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B3EWJ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XMM (Subject of Investigation/LOI) Query on XMM Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside C₁₄ H₁₅ Br Cl N O₆ OPIFSICVWOWJMJ-HAAGFXOZSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
MN (Subject of Investigation/LOI) Query on MN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.248 (Depositor), 0.250 (DCC)
R-Value Work: 0.201 (Depositor), 0.210 (DCC)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.35	α = 90
b = 109.414	β = 90
c = 126.364	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-11-29

Deposition Author(s):

Sacramento-Neto, J.C.

Van Damme, E.J.M.

Nascimento, K.S.

Cavada, B.S.

Funding Organization	Location	Grant Number
Coordination for the Improvement of Higher Education Personnel	Brazil	--
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	--
Research Foundation - Flanders (FWO)	Belgium	12T4622N