6TES

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

• PDB DOI: https://doi.org/10.2210/pdb6TES/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2019-11-12 Released: 2021-05-19 
• Deposition Author(s): Chiapparino, A., De Giorgi, F., Scietti, L., Faravelli, S., Roscioli, T., Forneris, F.
• Funding Organization(s): European Commission, Italian Association for Cancer Research, Other private, Italian Ministry of Education

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.238 
• R-Value Work: 0.190 
• R-Value Observed: 0.193 

Starting Model: experimental

Literature

Identification of Regulatory Molecular 'Hot Spots' for LH/PLOD Collagen Glycosyltransferase Activity

Mattoteia, D., Chiapparino, A., Fumagalli, M., De Marco, M., De Giorgi, F., Negro, L., Pinnola, A., Faravelli, S., Roscioli, T., Scietti, L., Forneris, F.

(2023) Int J Mol Sci 

• DOI: https://doi.org/10.3390/ijms241311213

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 84.45 kDa 
• Atom Count: 6,289 
• Modelled Residue Count: 700 
• Deposited Residue Count: 718 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3	A	718	Homo sapiens	Mutation(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 GTEx:  ENSG00000106397
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: O60568-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UGA (Subject of Investigation/LOI)	G [auth A]	URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID C15 H22 N2 O18 P2 HDYANYHVCAPMJV-LXQIFKJMSA-N
NAG	H [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
AKG (Subject of Investigation/LOI)	C [auth A]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
EDO	I [auth A], J [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE2 (Subject of Investigation/LOI)	D [auth A], E [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)	F [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.238 
• R-Value Work: 0.190 
• R-Value Observed: 0.193 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.202	α = 90
b = 100.505	β = 90
c = 224.745	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
STARANISO	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-05-19 
Deposition Author(s): Chiapparino, A., De Giorgi, F., Scietti, L., Faravelli, S., Roscioli, T., Forneris, F.

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Funding Organization	Location	Grant Number
European Commission		MSCA-IF 745934 - COTETHERS
Italian Association for Cancer Research	Italy	20075
Other private	Italy	The Giovanni Armenise-Harvard Foundation CDA 2013
Italian Ministry of Education	Italy	Dipartimenti di Eccellenza Program 2018-2022

Revision History  

• Version 1.0: 2021-05-19
  Type: Initial release
  
• Version 1.1: 2023-07-19
  Changes: Database references
• Version 1.2: 2024-02-07
  Changes: Data collection, Refinement description