4X5K | pdb_00004x5k

Human NAA50 complex with coenzyme A and an acetylated peptide

• PDB DOI: https://doi.org/10.2210/pdb4X5K/pdb

• Classification: Transferase/Peptide
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2014-12-05 Released: 2015-12-16 
• Deposition Author(s): Reddi, R., Addlagatta, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 
  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Human NAA50 with coenzymeA and a peptide

Reddi, R., Addlagatta, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 20.66 kDa 
• Atom Count: 1,320 
• Modeled Residue Count: 158 
• Deposited Residue Count: 174 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-alpha-acetyltransferase 50	A	169	Homo sapiens	Mutation(s): 0  Gene Names: NAA50, MAK3, NAT13, NAT5 EC: 2.3.1 (PDB Primary Data), 2.3.1.258 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZZ1 (Homo sapiens) Explore Q9GZZ1  Go to UniProtKB:  Q9GZZ1
PHAROS:  Q9GZZ1 GTEx:  ENSG00000121579

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ACE-MMAS	B	5	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	C [auth A]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
COA	BindingDB:  4X5K	Kd: 156 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.626	α = 90
b = 53.193	β = 90
c = 67.586	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-16 
Deposition Author(s): Reddi, R., Addlagatta, A.

Revision History  

• Version 1.0: 2015-12-16
  Type: Initial release
  
• Version 1.1: 2017-10-04
  Changes: Advisory, Data collection, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary