6FXT

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

• PDB DOI: https://doi.org/10.2210/pdb6FXT/pdb

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


• Deposited: 2018-03-09 Released: 2018-08-22 
• Deposition Author(s): Scietti, L., Chiapparino, A., De Giorgi, F., Fumagalli, M., Khoriauli, L., Nergadze, S., Basu, S., Olieric, V., Banushi, B., Giulotto, E., Gissen, P., Forneris, F.
• Funding Organization(s): The Giovanni Armenise-Harvard Foundation, Cariplo Foundation, AIRC, European Commission MSCA-IF, European Union - BIOSTRUCT

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.248 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS, gel filtration, homology

Macromolecule Content

• Total Structure Weight: 84.33 kDa 
• Atom Count: 5,996 
• 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
UniProt & NIH Common Fund Data Resources
Find proteins for O60568 (Homo sapiens) Explore O60568  Go to UniProtKB:  O60568
PHAROS:  O60568 GTEx:  ENSG00000106397

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
UDP (Subject of Investigation/LOI)	F [auth A]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
NAG	J [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
AKG (Subject of Investigation/LOI)	E [auth A]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE2 (Subject of Investigation/LOI)	G [auth A], H [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)	I [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.248 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.744	α = 90
b = 100.472	β = 90
c = 225.394	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
SHARP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-08-22 
Deposition Author(s): Scietti, L., Chiapparino, A., De Giorgi, F., Fumagalli, M., Khoriauli, L., Nergadze, S., Basu, S., Olieric, V., Banushi, B., Giulotto, E., Gissen, P., Forneris, F.

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Funding Organization	Location	Grant Number
The Giovanni Armenise-Harvard Foundation	United States	Career Development Award
Cariplo Foundation	Italy	2015-0768 - COME TRUE
AIRC	Italy	20075
European Commission MSCA-IF	Italy	745934 - COTETHERS
European Union - BIOSTRUCT	Italy	7551, 10205

Revision History  

• Version 1.0: 2018-08-22
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary