2W4M | pdb_00002w4m

The Crystal Structure of human N-acetylneuraminic acid phosphatase, NANP

• PDB DOI: https://doi.org/10.2210/pdb2W4M/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-11-28 Released: 2008-12-23 
• Deposition Author(s): Ugochukwu, E., Cocking, R., Yue, W.W., Pike, A.C.W., Roos, A., Muniz, J.R.C., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Oppermann, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.212 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

The Crystal Structure of Human N-Acetylneuraminic Acid Phosphatase, Nanp

Ugochukwu, E., Cocking, R., Yue, W.W., Pike, A.C.W., Roos, A., Muniz, J.R.C., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., 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 PQS (software)

Macromolecule Content 

• Total Structure Weight: 30.69 kDa 
• Atom Count: 2,054 
• Modeled Residue Count: 250 
• Deposited Residue Count: 270 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-ACYLNEURAMINATE-9-PHOSPHATASE	A	270	Homo sapiens	Mutation(s): 0  EC: 3.1.3.29
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TBE9 (Homo sapiens) Explore Q8TBE9  Go to UniProtKB:  Q8TBE9
PHAROS:  Q8TBE9 GTEx:  ENSG00000170191

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A], F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.212 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.74	α = 90
b = 122.74	β = 90
c = 74.55	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-23 
Deposition Author(s): Ugochukwu, E., Cocking, R., Yue, W.W., Pike, A.C.W., Roos, A., Muniz, J.R.C., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Oppermann, U.

Revision History  

• Version 1.0: 2008-12-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2019-05-08
  Changes: Data collection, Experimental preparation
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description