6TEC

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

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
Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3A718Homo sapiensMutation(s): 0 
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
UDX
Query on UDX

Download Ideal Coordinates CCD File 
C [auth A]URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE
C14 H22 N2 O16 P2
DQQDLYVHOTZLOR-OCIMBMBZSA-N
 Ligand Interaction
NAG
Query on NAG

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

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

Download Ideal Coordinates CCD File 
I [auth A], J [auth A], K [auth A], L [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download Ideal Coordinates CCD File 
E [auth A], F [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.264α = 90
b = 99.987β = 90
c = 223.96γ = 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