5SSY | pdb_00005ssy

Crystal Structure of human formylglycine generating enzyme

• PDB DOI: https://doi.org/10.2210/pdb5SSY/pdb
• Deposition Group: G_1002243 | Explore  G_1002243  

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2022-08-12 Released: 2023-08-23 
• Deposition Author(s): Radhakrishnan, K., Schlotawa, L., Rudolph, M.G.
• Funding Organization(s): University of Bielefeld

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: other

Literature

Crystal Structure of human formylglycine generating enzyme in complex with N-acetyl-cysteine methylester

Kowal, J., Schlotawa, L., Rudolph, M.G., Niemann, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 36.67 kDa 
• Atom Count: 2,684 
• Modeled Residue Count: 277 
• Deposited Residue Count: 323 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formylglycine-generating enzyme	A	323	Homo sapiens	Mutation(s): 0  Gene Names: SUMF1, PSEC0152, UNQ3037/PRO9852 EC: 1.8.3.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NBK3 (Homo sapiens) Explore Q8NBK3  Go to UniProtKB:  Q8NBK3
PHAROS:  Q8NBK3 GTEx:  ENSG00000144455
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: Q8NBK3-1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
UG6 (Subject of Investigation/LOI)	F [auth A]	methyl N-acetyl-L-cysteinate C6 H11 N O3 S QTKAQJWFVXPIFV-YFKPBYRVSA-N
CU1	B [auth A]	COPPER (I) ION Cu VMQMZMRVKUZKQL-UHFFFAOYSA-N
CA	D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.475	α = 90
b = 61.731	β = 90
c = 109.719	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-23 
Deposition Author(s): Radhakrishnan, K., Schlotawa, L., Rudolph, M.G.

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Funding Organization	Location	Grant Number
University of Bielefeld	Germany	--

Revision History  

• Version 1.0: 2023-08-23
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Structure summary
• Version 1.2: 2024-10-23
  Changes: Structure summary
• Version 1.3: 2026-02-18
  Changes: Refinement description