5BYN | pdb_00005byn

Canavalia maritima lectin complexed with synthetic selenoamino acid

PDB DOI: https://doi.org/10.2210/pdb5BYN/pdb

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

Deposited: 2015-06-10 Released: 2015-11-18
Deposition Author(s): Nobrega, R.B., Silva-Filho, J.C., Kawasoko, C.Y., Rodrigues, O.E.D., Schwab, R.S., Braga, A.L., Delatorre, P., Cavada, B.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.278 (Depositor), 0.291 (DCC)
R-Value Work:
0.204 (Depositor), 0.229 (DCC)
R-Value Observed:
0.207 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Canavalia maritima lectin complexed with synthetic selenoamino acid

Nobrega, R.B., Silva-Filho, J.C., Kawasoko, C.Y., Rodrigues, O.E.D., Schwab, R.S., Braga, A.L., Delatorre, P., Cavada, B.S.

To be published.

Macromolecule Content

Total Structure Weight: 52.4 kDa
Atom Count: 3,722
Modeled Residue Count: 472
Deposited Residue Count: 474
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Concanavalin-A	A, B	237	Canavalia lineata	Mutation(s): 0
UniProt
Find proteins for P81460 (Canavalia lineata) Explore P81460 Go to UniProtKB: P81460
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P81460
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4WM Query on 4WM Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B]	H [auth A], I [auth B]	(4R)-4-{[(S)-tert-butoxy(hydroxy)methyl]amino}-5-[(1S)-cyclohex-2-en-1-ylselanyl]pentane-1,1-diol C₁₆ H₃₁ N O₄ Se UREOHWFKMYYNAM-NFAWXSAZSA-N		Interactions Focus chain H [auth A] Focus chain I [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth B]
CD Query on CD 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]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
PEG Query on PEG 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]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	G [auth A], L [auth B], M [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain K [auth B]	D [auth A], K [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-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]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B]	C [auth A], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.278 (Depositor), 0.291 (DCC)
R-Value Work: 0.204 (Depositor), 0.229 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 190.64	α = 90
b = 190.64	β = 90
c = 190.64	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-11-18

Deposition Author(s):

Silva-Filho, J.C.

Rodrigues, O.E.D.

Revision History (Full details and data files)

Version 1.0: 2015-11-18
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references, Derived calculations

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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.