7UOD | pdb_00007uod

Crystal structure of a lectin from Canavalia maritima seed (ConM) complexed with 2,4-dichloro-phenoxyacetic acid

PDB DOI: https://doi.org/10.2210/pdb7UOD/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Canavalia rosea
Mutation(s): No

Deposited: 2022-04-12 Released: 2023-04-19
Deposition Author(s): Sousa, J.P., Bezerra, E.H.S., Sales, M.V., Queiroz, P.P., da Silva, F.M.S., Carvalho, C.P.S., Freire, V.N., Rocha, B.A.M.
Funding Organization(s): Brazilian National Council for Scientific and Technological Development (CNPq)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.227 (Depositor), 0.214 (DCC)
R-Value Work:
0.199 (Depositor)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural analysis of Canavalia maritima lectin complexed with auxins

Sousa, J.P., Bezerra, E.H.S., Sales, M.V., Queiroz, P.P., da Silva, F.M.S., Carvalho, C.P.S., Freire, V.N., Rocha, B.A.M.

To be published.

Macromolecule Content

Total Structure Weight: 52.14 kDa
Atom Count: 3,920
Modeled Residue Count: 467
Deposited Residue Count: 474
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ConM	A, B	237	Canavalia rosea	Mutation(s): 0
UniProt
Find proteins for A0A6M6R659 (Canavalia rosea) Explore A0A6M6R659 Go to UniProtKB: A0A6M6R659
Find proteins for A0A8E6Z6W6 (Canavalia rosea) Explore A0A8E6Z6W6 Go to UniProtKB: A0A8E6Z6W6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	A0A6M6R659 A0A8E6Z6W6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CFA (Subject of Investigation/LOI) Query on CFA Download:Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	(2,4-DICHLOROPHENOXY)ACETIC ACID C₈ H₆ Cl₂ O₃ OVSKIKFHRZPJSS-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain G [auth A] MOL2 format, chain O [auth B] MOL2 format, chain G [auth A] mmCIF format, chain O [auth B] mmCIF format, chain G [auth A]	G [auth A], O [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain O [auth B] Interactions & Density Focus chain G [auth A] Focus chain O [auth B]
DBB (Subject of Investigation/LOI) Query on DBB Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain C [auth A]	C [auth A], J [auth B]	D-ALPHA-AMINOBUTYRIC ACID C₄ H₉ N O₂ QWCKQJZIFLGMSD-GSVOUGTGSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B]	F [auth A], M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain M [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B]	E [auth A], L [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain D [auth A]	D [auth A], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain K [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], P [auth B], Q [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B]