4P14 | pdb_00004p14

Crystal structure of Canavalia brasiliensis (ConBr) complexed with adenine

PDB DOI: https://doi.org/10.2210/pdb4P14/pdb

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

Deposited: 2014-02-24 Released: 2015-04-15
Deposition Author(s): Delatorre, P., Rocha, B.A.M., Silva-Filho, J.C., Teixeira, C.S., Cavada, B.S., Nascimento, K.S., Neto, I.L.B., Nobrega, R.B., Nagano, C.S., Sampaio, A.H., Holanda, E., Leal, R.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.228 (Depositor), 0.233 (DCC)
R-Value Work:
0.175 (Depositor), 0.188 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Canavalia brasiliensis (ConBr) complexed with adenine

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

To be published.

Macromolecule Content

Total Structure Weight: 26.23 kDa
Atom Count: 1,918
Modeled Residue Count: 236
Deposited Residue Count: 237
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Concanavalin-Br	A	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
ADE Query on ADE Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ADENINE C₅ H₅ N₅ GFFGJBXGBJISGV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
DBB Query on DBB 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]	D-ALPHA-AMINOBUTYRIC ACID C₄ H₉ N O₂ QWCKQJZIFLGMSD-GSVOUGTGSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth A]	E [auth A], I [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth A] Interactions & Density Focus chain E [auth A] Focus chain I [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.228 (Depositor), 0.233 (DCC)
R-Value Work: 0.175 (Depositor), 0.188 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.12	α = 90
b = 70.94	β = 90
c = 97.43	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-04-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-04-15
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy
Version 1.2: 2023-11-15
Changes: Data collection