4PCR

Crystal structure of Canavalia brasiliensis seed lectin (ConBr) complexed with Gamma-Aminobutyric Acid (GABA)

PDB DOI: https://doi.org/10.2210/pdb4PCR/pdb

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

Deposited: 2014-04-16 Released: 2015-04-22
Deposition Author(s): Delatorre, P., Rocha, B.A.M., Silva-Filho, J.C., Teixeira, C.S., Cavada, B.S., Nascimento, K.S., Nbrega, R.B., Nagano, C.S., Sampaio, A.H., Leal, R.B., Neto, I.L.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.236
R-Value Work: 0.200
R-Value Observed: 0.204

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Crystal structure of Canavalia brasiliensis seed lectin (ConBr) complexed with Gamma-Aminobutyric Acid (GABA)

Delatorre, P., Rocha, B.A.M., Silva-Filho, J.C., Teixeira, C.S., Cavada, B.S., Nascimento, K.S., Nbrega, R.B., Nagano, C.S., Sampaio, A.H., Leal, R.B., Neto, I.L.B.

To be published.

Macromolecule Content

Total Structure Weight: 52.25 kDa
Atom Count: 3,706
Modelled Residue Count: 466
Deposited Residue Count: 474
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Concanavalin-Br	A, B [auth D]	237	Canavalia brasiliensis	Mutation(s): 0
UniProt
Find proteins for P55915 (Canavalia brasiliensis) Explore P55915 Go to UniProtKB: P55915
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P55915
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth D] SDF format, chain P [auth D] MOL2 format, chain H [auth A] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] mmCIF format, chain H [auth A] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D]	H [auth A], O [auth D], P [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain H [auth A] Focus chain O [auth D] Focus chain P [auth D]
ABU Query on ABU Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth D]	F [auth A], G [auth A], L [auth D]	GAMMA-AMINO-BUTANOIC ACID C₄ H₉ N O₂ BTCSSZJGUNDROE-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain N [auth D] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D]	M [auth D], N [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain M [auth D] Focus chain N [auth D]
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain K [auth D]	E [auth A], K [auth D]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth D]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth D] MOL2 format, chain D [auth A] MOL2 format, chain J [auth D] mmCIF format, chain D [auth A] mmCIF format, chain J [auth D]	D [auth A], J [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain J [auth D] Interactions & Density Focus chain D [auth A] Focus chain J [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth D] MOL2 format, chain C [auth A] MOL2 format, chain I [auth D] mmCIF format, chain C [auth A] mmCIF format, chain I [auth D]	C [auth A], I [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain I [auth D] Interactions & Density Focus chain C [auth A] Focus chain I [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.236
R-Value Work: 0.200
R-Value Observed: 0.204
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.41	α = 90
b = 72.13	β = 124.47
c = 68.39	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2015-04-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-04-22
Type: Initial release
Version 1.1: 2015-10-14
Changes: Data collection
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection