4JKX

Crystal structure Mistletoe Lectin I from Viscum album in complex with kinetin at 2.35 A resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view detailsBest fitted H35Click on this verticalbar to view details

This is version 2.2 of the entry. See complete history


Literature

Crystal structure Mistletoe Lectin I from Viscum album in complex with kinetin at 2.35 A resolution.

Prokofev, I.I.Lashkov, A.A.Gabdoulkhakov, A.G.Meyer, A.Barciszewski, J.Betzel, C.Mikhailov, A.M.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-galactoside-specific lectin 1 A chain249Viscum albumMutation(s): 0 
EC: 3.2.2.22
UniProt
Find proteins for P81446 (Viscum album)
Explore P81446 
Go to UniProtKB:  P81446
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP81446
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-galactoside-specific lectin 1 B chain263Viscum albumMutation(s): 0 
EC: 3.2.2.22
UniProt
Find proteins for P81446 (Viscum album)
Explore P81446 
Go to UniProtKB:  P81446
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP81446
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G47362BJ
GlyCosmos:  G47362BJ
GlyGen:  G47362BJ
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A],
S [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
H35
Query on H35

Download Ideal Coordinates CCD File 
I [auth A]N-(FURAN-2-YLMETHYL)-7H-PURIN-6-AMINE
C10 H9 N5 O
QANMHLXAZMSUEX-UHFFFAOYSA-N
SO4
Query on SO4

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E [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
EA [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DIO
Query on DIO

Download Ideal Coordinates CCD File 
K [auth A]1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
J [auth A]
T [auth B]
U [auth B]
V [auth B]
W [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
AZI
Query on AZI

Download Ideal Coordinates CCD File 
R [auth B]AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
FA [auth B],
Q [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.01α = 90
b = 107.01β = 90
c = 312.42γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DNAdata collection
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view detailsBest fitted H35Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-21
    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: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-10-30
    Changes: Structure summary