5BYN

Canavalia maritima lectin complexed with synthetic selenoamino acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Concanavalin-A
A, B
237Canavalia lineataMutation(s): 0 
UniProt
Find proteins for P81460 (Canavalia lineata)
Explore P81460 
Go to UniProtKB:  P81460
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP81460
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4WM
Query on 4WM

Download Ideal Coordinates CCD File 
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
CD
Query on CD

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E [auth A]CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
PEG
Query on PEG

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F [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

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G [auth A],
L [auth B],
M [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN
Query on MN

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D [auth A],
K [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA
Query on CA

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C [auth A],
J [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: F 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 190.64α = 90
b = 190.64β = 90
c = 190.64γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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