4H55 | pdb_00004h55

Crystal structure of Canavalia brasiliensis seed lectin (ConBr) in complex with beta-d-ribofuranose

• PDB DOI: https://doi.org/10.2210/pdb4H55/pdb
• Entry: 4H55 supersedes: 4DPS

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


• Deposited: 2012-09-18 Released: 2012-10-31 
• Deposition Author(s): Salviano, E., Rocha, B.A.M., Cavada, B.S., Delatorre, P., Santi-Gadelha, T., Gadelha, C.A.A., Silva-Filho, J.C., Nobrega, R.B., Farias, D.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.227 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

Crystal structure of Canavalia brasiliensis seed lectin (ConBr) in complex with beta-d-ribofuranose

Salviano, E., Rocha, B.A.M., Cavada, B.S., Delatorre, P., Santi-Gadelha, T., Gadelha, C.A.A., Silva-Filho, J.C., Nobrega, R.B., Farias, D.L.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 25.94 kDa 
• Atom Count: 1,874 
• Modeled Residue Count: 233 
• Deposited Residue Count: 237 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BDR	D [auth A]	beta-D-ribofuranose C5 H10 O5 HMFHBZSHGGEWLO-TXICZTDVSA-N
DBB	E [auth A]	D-ALPHA-AMINOBUTYRIC ACID C4 H9 N O2 QWCKQJZIFLGMSD-GSVOUGTGSA-N
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.227 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.24	α = 90
b = 70.43	β = 90
c = 97.57	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-31 
Deposition Author(s): Salviano, E., Rocha, B.A.M., Cavada, B.S., Delatorre, P., Santi-Gadelha, T., Gadelha, C.A.A., Silva-Filho, J.C., Nobrega, R.B., Farias, D.L.
• This entry supersedes: 4DPS

Revision History  

• Version 1.0: 2012-10-31
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-02-28
  Changes: Data collection, Database references, Structure summary