4ML4

Crystal structure of the complex of signaling glycoprotein from buffalo (SPB-40) with tetrahydropyran at 2.5 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.247 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of the complex of signaling glycoprotein from buffalo (SPB-40) with tetrahydropyran at 2.5 A resolution

Yamini, S.Chaudhary, A.Sinha, M.Kaur, P.Sharma, S.Singh, T.P.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Chitinase-3-like protein 1A361Bubalus bubalisMutation(s): 0 
Gene Names: CHI3L1MGP-40
UniProt
Find proteins for Q7YS85 (Bubalus bubalis)
Explore Q7YS85 
Go to UniProtKB:  Q7YS85
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
B [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PYE
Query on PYE

Download Ideal Coordinates CCD File 
C [auth A]TETRAHYDROPYRAN
C5 H10 O
DHXVGJBLRPWPCS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.247 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.174α = 90
b = 67.088β = 90
c = 106.569γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-25
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary