6TEX

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


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
Expand
  • 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
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UDP (Subject of Investigation/LOI)
Query on UDP

Download Ideal Coordinates CCD File 
F [auth A]URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
J [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
AKG (Subject of Investigation/LOI)
Query on AKG

Download Ideal Coordinates CCD File 
E [auth A]2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FE2 (Subject of Investigation/LOI)
Query on FE2

Download Ideal Coordinates CCD File 
G [auth A], H [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
MN (Subject of Investigation/LOI)
Query on MN

Download Ideal Coordinates CCD File 
I [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.049α = 90
b = 100.409β = 90
c = 225.179γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
STARANISOdata scaling

Structure Validation

View Full Validation Report




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