6TEU

Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Val80Lys mutant - Cocrystal with Fe2+, Mn2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

A cooperative network of molecular "hot spots" highlights the complexity of LH3 collagen glycosyltransferase activities

Chiapparino, A.De Giorgi, F.Scietti, L.Faravelli, S.Roscioli, T.Forneris, F.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3A718Homo sapiensMutation(s): 1 
Gene Names: PLOD3
EC: 1.14.11.4 (PDB Primary Data), 2.4.1.50 (PDB Primary Data), 2.4.1.66 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O60568 (Homo sapiens)
Explore O60568 
Go to UniProtKB:  O60568
PHAROS:  O60568
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.004α = 90
b = 100.691β = 90
c = 225.674γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
STARANISOdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionMSCA-IF 745934 - COTETHERS
Italian Association for Cancer ResearchItaly20075
Other privateItalyThe Giovanni Armenise-Harvard Foundation CDA 2013
Italian Ministry of EducationItalyDipartimenti di Eccellenza Program 2018-2022

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-19
    Type: Initial release