6TE3 | pdb_00006te3

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

PDB DOI: https://doi.org/10.2210/pdb6TE3/pdb

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

Deposited: 2019-11-11 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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.246 (Depositor), 0.287 (DCC)
R-Value Work:
0.194 (Depositor), 0.247 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 84.02 kDa
Atom Count: 5,874
Modeled Residue Count: 686
Deposited Residue Count: 718
Unique protein chains: 1

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O60568
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A	Go to GlyGen: O60568-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
AKG (Subject of Investigation/LOI) Query on AKG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	2-OXOGLUTARIC ACID C₅ H₆ O₅ KPGXRSRHYNQIFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
FE2 (Subject of Investigation/LOI) Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.246 (Depositor), 0.287 (DCC)
R-Value Work: 0.194 (Depositor), 0.247 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.995	α = 90
b = 100.035	β = 90
c = 225.208	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-05-19

Deposition Author(s):

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 (Full details and data files)

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
Version 2.0: 2025-10-01
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary