4DIQ | pdb_00004diq

Crystal Structure of human NO66

• PDB DOI: https://doi.org/10.2210/pdb4DIQ/pdb

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


• Deposited: 2012-01-31 Released: 2012-03-07 
• Deposition Author(s): Vollmar, M., Krojer, T., Ng, S., Pilka, E., Bray, J., Pike, A.C.W., Filippakopoulos, P., Roos, A., Arrowsmith, C.H., Edwards, E., Bountra, C., von Delft, F., Oppermann, U., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Crystal Structure of human NO66

Vollmar, M., Krojer, T., Stan, N.G., Pilka, E., Phillips, C., Burgess-Brown, N., Bray, J., Pike, A.C.W., Filippakopoulos, P., Roos, A., Arrowsmith, C.H., Edwards, A., Bountra, C., von Delft, F., Oppermann, U.

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)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 111.89 kDa 
• Atom Count: 7,412 
• Modeled Residue Count: 916 
• Deposited Residue Count: 978 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase NO66	A, B	489	Homo sapiens	Mutation(s): 1  Gene Names: NO66, C14orf169 EC: 1.14.11.27 (PDB Primary Data), 1.14.11.79 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H6W3 (Homo sapiens) Explore Q9H6W3  Go to UniProtKB:  Q9H6W3
PHAROS:  Q9H6W3 GTEx:  ENSG00000170468

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PD2	D [auth A], F [auth B]	PYRIDINE-2,4-DICARBOXYLIC ACID C7 H5 N O4 MJIVRKPEXXHNJT-UHFFFAOYSA-N
SO4	G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NI	C [auth A], E [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.674	α = 90
b = 149.55	β = 90
c = 105.311	γ = 90

Software Package:

Software Name	Purpose
not	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-07 
Deposition Author(s): Vollmar, M., Krojer, T., Ng, S., Pilka, E., Bray, J., Pike, A.C.W., Filippakopoulos, P., Roos, A., Arrowsmith, C.H., Edwards, E., Bountra, C., von Delft, F., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2012-03-07
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references
• Version 1.2: 2022-12-21
  Changes: Database references, Derived calculations
• Version 1.3: 2024-05-22
  Changes: Data collection