6XFQ | pdb_00006xfq

Structure of a novel antithrombotic agent Agkisacucetin in complex with the platelet glycoprotein Ib receptor

• PDB DOI: https://doi.org/10.2210/pdb6XFQ/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens, Deinagkistrodon acutus
• Expression System: Cricetulus griseus, Komagataella pastoris
• Mutation(s): No 


• Deposited: 2020-06-16 Released: 2021-06-23 
• Deposition Author(s): Wang, J., Gao, Y.X., Ke, J.Y., Zhu, Z.L., Niu, L.W.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.311 (Depositor), 0.311 (DCC) 
• R-Value Work: 
  0.275 (Depositor), 0.275 (DCC) 
• R-Value Observed: 
  0.276 (Depositor) 

Starting Models: experimental

Literature

Structure of a novel antithrombotic agent Agkisacucetin in complex with the platelet glycoprotein Ib receptor

Wang, J., Gao, Y.X., Ke, J.Y., Zhu, Z.L., Niu, L.W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content 

• Total Structure Weight: 68.6 kDa 
• Atom Count: 4,128 
• Modeled Residue Count: 527 
• Deposited Residue Count: 608 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Platelet glycoprotein Ib alpha chain	A [auth G]	305	Homo sapiens	Mutation(s): 0  Gene Names: GP1BA
UniProt & NIH Common Fund Data Resources
Find proteins for P07359 (Homo sapiens) Explore P07359  Go to UniProtKB:  P07359
PHAROS:  P07359 GTEx:  ENSG00000185245

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Snaclec agglucetin subunit alpha-1	B [auth A]	154	Deinagkistrodon acutus	Mutation(s): 0
UniProt
Find proteins for Q8JIV9 (Deinagkistrodon acutus) Explore Q8JIV9  Go to UniProtKB:  Q8JIV9

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Snaclec agglucetin subunit beta-2	C [auth B]	149	Deinagkistrodon acutus	Mutation(s): 0
UniProt
Find proteins for Q8AYA3 (Deinagkistrodon acutus) Explore Q8AYA3  Go to UniProtKB:  Q8AYA3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.311 (Depositor), 0.311 (DCC) 
• R-Value Work:  0.275 (Depositor), 0.275 (DCC) 
• R-Value Observed: 0.276 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.304	α = 90
b = 86.304	β = 90
c = 189.963	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-06-23 
Deposition Author(s): Wang, J., Gao, Y.X., Ke, J.Y., Zhu, Z.L., Niu, L.W.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	U1632124

Revision History  

• Version 1.0: 2021-06-23
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary