4LDK | pdb_00004ldk

FAD-linked sulfhydryl oxidase ALR mutation

• PDB DOI: https://doi.org/10.2210/pdb4LDK/pdb

• Classification: FLAVOPROTEIN, OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-06-24 Released: 2014-07-16 
• Deposition Author(s): Dong, M., Ramadan, S., Thorpe, C., Bahnson, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.267 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

FAD-linked sulfhydryl oxidase ALR mutation

Dong, M., Ramadan, S., Thorpe, C., Bahnson, B.

To be published.

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)

Macromolecule Content

• Total Structure Weight: 15.89 kDa 
• Atom Count: 1,079 
• Modelled Residue Count: 115 
• Deposited Residue Count: 126 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FAD-linked sulfhydryl oxidase ALR	A	126	Homo sapiens	Mutation(s): 3  Gene Names: GFER, ALR, HERV1, HPO EC: 1.8.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for P55789 (Homo sapiens) Explore P55789  Go to UniProtKB:  P55789
PHAROS:  P55789 GTEx:  ENSG00000127554

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.267 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.897	α = 90
b = 77.77	β = 90
c = 62.772	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-16 
Deposition Author(s): Dong, M., Ramadan, S., Thorpe, C., Bahnson, B.

Revision History  

• Version 1.0: 2014-07-16
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary