1S1D | pdb_00001s1d

Structure and protein design of human apyrase

PDB DOI: https://doi.org/10.2210/pdb1S1D/pdb

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

Deposited: 2004-01-06 Released: 2004-03-16
Deposition Author(s): Dai, J., Liu, J., Deng, Y., Smith, T.M., Lu, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.194 (Depositor), 0.194 (DCC)
R-Value Work:
0.164 (Depositor), 0.165 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure and protein design of a human platelet function inhibitor.

Dai, J., Liu, J., Deng, Y., Smith, T.M., Lu, M.

(2004) Cell 116: 649-659

PubMed: 15006348 Search on PubMed
DOI: https://doi.org/10.1016/s0092-8674(04)00172-2
Primary Citation Related Structures:
1S18, 1S1D

PubMed Abstract:
Hematophagous arthropods secrete a salivary apyrase that inhibits platelet activation by catabolizing ADP released from damaged tissues and blood cells. We report the X-ray crystal structures of a human enzyme of the soluble apyrase family in its apo state and bound to a substrate analog. The structures reveal a nucleotide binding domain comprising a five-blade beta propeller, binding determinants of the substrate and the active site, and an unusual calcium binding site with a potential regulatory function. Using a comparative structural biology approach, we were able to redesign the human apyrase so as to enhance its ADPase activity by more than 100-fold. The engineered enzyme is a potent inhibitor of platelet aggregation and may serve as the basis for the development of a new class of antithrombotic agents.

Organizational Affiliation

Department of Biochemistry, Weill Medical College of Cornell University, New York, NY 10021, USA.

Macromolecule Content

Total Structure Weight: 76.15 kDa
Atom Count: 5,776
Modeled Residue Count: 632
Deposited Residue Count: 662
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
apyrase	A, B	331	Homo sapiens	Mutation(s): 0 Gene Names: SHAPY EC: 3.6.1.5 (PDB Primary Data), 3.6.1.6 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WVQ1 (Homo sapiens) Explore Q8WVQ1 Go to UniProtKB: Q8WVQ1
PHAROS: Q8WVQ1 GTEx: ENSG00000171302
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8WVQ1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GP2 Query on GP2 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] mmCIF format, chain E [auth A] mmCIF format, chain M [auth B]	E [auth A], M [auth B]	PHOSPHOMETHYLPHOSPHONIC ACID GUANOSYL ESTER C₁₁ H₁₇ N₅ O₁₀ P₂ OCJWYBKRHNXUME-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain M [auth B]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	F [auth A] G [auth A] H [auth A] I [auth A] N [auth B] F [auth A], G [auth A], H [auth A], I [auth A], N [auth B], O [auth B], P [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	K [auth B], L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain K [auth B] Focus chain L [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B]	C [auth A], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.194 (Depositor), 0.194 (DCC)
R-Value Work: 0.164 (Depositor), 0.165 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.163	α = 98.99
b = 52.45	β = 106.99
c = 77.478	γ = 100.09

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2004-03-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-03-16
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description