6FXY
Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Cocrystal with Fe2+, Mn2+, UDP-Gal - Structure from long-wavelength S-SAD
- PDB DOI: https://doi.org/10.2210/pdb6FXY/pdb
- Classification: TRANSFERASE
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2018-03-09 Released: 2018-08-22 
- Funding Organization(s): The Giovanni Armenise-Harvard Foundation, Cariplo Foundation, AIRC, European Commission MSCA-IF, European Union - BIOSTRUCT
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.14 Å
- R-Value Free: 0.231 
- R-Value Work: 0.194 
- R-Value Observed: 0.196 
This is version 2.0 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 | ||
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 | |
UDP (Subject of Investigation/LOI) Query on UDP | F [auth A] | URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N | |||
NAG Query on NAG | J [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
AKG (Subject of Investigation/LOI) Query on AKG | E [auth A] | 2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N | |||
GOL Query on GOL | C [auth A], D [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
FE2 (Subject of Investigation/LOI) Query on FE2 | G [auth A], H [auth A] | FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N | |||
MN (Subject of Investigation/LOI) Query on MN | I [auth A] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.14 Å
- R-Value Free: 0.231 
- R-Value Work: 0.194 
- R-Value Observed: 0.196 
- Space Group: C 2 2 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 97.04 | α = 90 |
b = 100.105 | β = 90 |
c = 224.743 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |
CRANK2 | phasing |
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.
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 (Full details and data files)
- 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