4PCR | pdb_00004pcr

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 (Depositor), 0.263 (DCC)
R-Value Work:
0.200 (Depositor), 0.223 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
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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
Modeled Residue Count: 466
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
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 O [auth D] SDF format, chain P [auth D] SDF format, chain H [auth A] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain H [auth A] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain H [auth A]	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 L [auth D] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain G [auth A]	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 J [auth D] SDF format, chain D [auth A] MOL2 format, chain J [auth D] MOL2 format, chain D [auth A] mmCIF format, chain J [auth D] mmCIF format, chain D [auth A]	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 (Depositor), 0.263 (DCC)
R-Value Work: 0.200 (Depositor), 0.223 (DCC)
R-Value Observed: 0.204 (Depositor)

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

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View more in-depth experimental data

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