5HDE

Crystal Structure of PTPN12 Catalytic Domain

• PDB DOI: https://doi.org/10.2210/pdb5HDE/pdb

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


• Deposited: 2016-01-05 Released: 2017-01-18 
• Deposition Author(s): Dong, H., Li, S., Shi, J.
• Funding Organization(s): the National Natural Science Foundation of China, the PUMC Youth Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.213 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of PTPN12 Catalytic Domain

Dong, H., Shi, J., Li, J., Li, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 36.5 kDa 
• Atom Count: 2,883 
• Modelled Residue Count: 300 
• Deposited Residue Count: 307 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase non-receptor type 12	A	307	Homo sapiens	Mutation(s): 0  Gene Names: PTPN12 EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q05209 (Homo sapiens) Explore Q05209  Go to UniProtKB:  Q05209
PHAROS:  Q05209 GTEx:  ENSG00000127947

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSP	A	L-PEPTIDE LINKING	C3 H8 N O5 P S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.213 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.01	α = 90
b = 40.967	β = 116.63
c = 75.686	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-01-18 
Deposition Author(s): Dong, H., Li, S., Shi, J.

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Funding Organization	Location	Grant Number
the National Natural Science Foundation of China	China	31300601
the PUMC Youth Fund	China	33320140186

Revision History  

• Version 1.0: 2017-01-18
  Type: Initial release
  
• Version 1.1: 2017-10-04
  Changes: Data collection
• Version 1.2: 2017-10-11
  Changes: Data collection
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Refinement description