6TEC
Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Cocrystal with Fe2+, Mn2+, UDP-Xylose
- PDB DOI: https://doi.org/10.2210/pdb6TEC/pdb
- Classification: TRANSFERASE
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2019-11-11 Released: 2021-05-19 
- Funding Organization(s): European Commission, Italian Association for Cancer Research, Other private, Italian Ministry of Education
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 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 1.2 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | O60568 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 6 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
UDX (Subject of Investigation/LOI) Query on UDX | C [auth A] | URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE C14 H22 N2 O16 P2 DQQDLYVHOTZLOR-OCIMBMBZSA-N | |||
NAG Query on NAG | H [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
AKG (Subject of Investigation/LOI) Query on AKG | D [auth A] | 2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N | |||
EDO Query on EDO | I [auth A], J [auth A], K [auth A], L [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N | |||
FE2 (Subject of Investigation/LOI) Query on FE2 | E [auth A], F [auth A] | FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N | |||
MN (Subject of Investigation/LOI) Query on MN | G [auth A] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |
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 = 97.264 | α = 90 |
b = 99.987 | β = 90 |
c = 223.96 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |
STARANISO | data scaling |
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.
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