6ARH | pdb_00006arh

Crystal structure of Human NAL at a resolution of 1.6 Angstrom

• PDB DOI: https://doi.org/10.2210/pdb6ARH/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-08-22 Released: 2018-08-22 
• Deposition Author(s): Pearce, F.G., Bundela, R., Keown, J.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.189 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Human NAL at a resolution of 1.6 Angstrom

Pearce, F.G., Bundela, R., Keown, J.R.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 149.54 kDa 
• Atom Count: 10,729 
• Modeled Residue Count: 1,204 
• Deposited Residue Count: 1,352 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetylneuraminate lyase	A, B, C, D	338	Homo sapiens	Mutation(s): 0  Gene Names: NPL, C1orf13 EC: 4.1.3.3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BXD5 (Homo sapiens) Explore Q9BXD5  Go to UniProtKB:  Q9BXD5
PHAROS:  Q9BXD5 GTEx:  ENSG00000135838

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	E [auth A], F [auth A], G [auth B], H [auth C], I [auth C], J [auth C], K [auth D], L [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.189 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.988	α = 90
b = 106.897	β = 90
c = 127.027	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-22 
Deposition Author(s): Pearce, F.G., Bundela, R., Keown, J.R.

Revision History  

• Version 1.0: 2018-08-22
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description