6TGG

scFv-1SM3 in complex with glycopeptide containing an sp2-imino sugar


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Synthesis, Conformational Analysis and in vivo Assays of an Anti-cancer Vaccine that features an Unnatural Antigen based on a sp2-Iminosugar Fragment

Corzana, F.Bermejo, I.A.Navo, C.D.Castro-Lopez, J.Guerreiro, A.Jimenez-Moreno, E.Sanchez-Fernandez, E.M.Garcia-Martin, F.Hinou, H.Nishimura, S.I.Garcia-Fernandez, J.M.M.Ortiz-Mellet, C.Avenoza, A.Busto, J.H.Bernardes, G.J.L.Hurtado-Guerrero, R.Peregrina, J.M.

(2020) Chem Sci 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ScFv_SM3A [auth H]244Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Mucin-1B [auth P]6Homo sapiensMutation(s): 0 
Gene Names: MUC1PUM
UniProt & NIH Common Fund Data Resources
Find proteins for P15941 (Homo sapiens)
Explore P15941 
Go to UniProtKB:  P15941
PHAROS:  P15941
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N8W
Query on N8W

Download Ideal Coordinates CCD File 
G [auth P]~{N}-[(6~{S},7~{R},8~{S},8~{a}~{R})-7,8-bis(oxidanyl)-3-oxidanylidene-1,5,6,7,8,8~{a}-hexahydro-[1,3]oxazolo[3,4-a]pyridin-6-yl]ethanamide
C9 H14 N2 O5
MKTHKMZBVDELIA-OSMVPFSASA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth H], D [auth H], E [auth H], F [auth H]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.271α = 90
b = 68.689β = 90
c = 90.393γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-08
    Type: Initial release