4BJO

Nitrate in the active site of PTP1b is a putative mimetic of the transition state

PDB DOI: https://doi.org/10.2210/pdb4BJO/pdb

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

Deposited: 2013-04-19 Released: 2014-02-12
Deposition Author(s): Kenny, P.W., Newman, J., Peat, T.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free: 0.239
R-Value Work: 0.215
R-Value Observed: 0.217

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Nitrate in the Active Site of Protein Tyrosine Phosphatase 1B is a Putative Mimetic of the Transition State.

Kenny, P.W., Newman, J., Peat, T.S.

(2014) Acta Crystallogr D Biol Crystallogr 70: 565

PubMed: 24531490 Search on PubMed
DOI: https://doi.org/10.1107/S1399004713031052
Primary Citation of Related Structures:
4BJO

PubMed Abstract:
The X-ray crystal structure of the complex of protein tyrosine phosphatase 1B with nitrate anion has been determined and modelled quantum-mechanically. Two protomers were present in the structure, one with the mechanistically important WPD loop closed and the other with this loop open. Nitrate was observed bound to each protomer, making close contacts with the S atom of the catalytic cysteine and a tyrosine residue from a crystallographically related protomer.

Organizational Affiliation

CSIRO Materials, Science and Engineering, 343 Royal Parade, Parkville, VIC 3052, Australia.

Macromolecule Content

Total Structure Weight: 79.07 kDa
Atom Count: 4,862
Modelled Residue Count: 571
Deposited Residue Count: 676
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 1	A, B	338	Homo sapiens	Mutation(s): 0 EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P18031 (Homo sapiens) Explore P18031 Go to UniProtKB: P18031
PHAROS: P18031 GTEx: ENSG00000196396
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P18031
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B]	F [auth A], K [auth B]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B]	C [auth A], D [auth A], I [auth B], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain I [auth B] Focus chain J [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth A]	E [auth A], H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth A] Interactions & Density Focus chain E [auth A] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free: 0.239
R-Value Work: 0.215
R-Value Observed: 0.217
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.62	α = 90
b = 66.765	β = 95.01
c = 68.771	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-02-12

Deposition Author(s):

Kenny, P.W.

Newman, J.

Peat, T.S.

Revision History (Full details and data files)

Version 1.0: 2014-02-12
Type: Initial release
Version 1.1: 2014-02-26
Changes: Database references
Version 1.2: 2019-05-08
Changes: Data collection, Experimental preparation, Other
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

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Help and Resources

4BJO

Nitrate in the active site of PTP1b is a putative mimetic of the transition state

Nitrate in the Active Site of Protein Tyrosine Phosphatase 1B is a Putative Mimetic of the Transition State.

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)