7PHX

Tsetse thrombin inhibitor in complex with human alpha-thrombin - acid-stable sulfotyrosine analogue

• PDB DOI: https://doi.org/10.2210/pdb7PHX/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens, Glossina morsitans morsitans
• Mutation(s): Yes 


• Deposited: 2021-08-18 Released: 2021-10-06 
• Deposition Author(s): Pereira, P.J.B., Ripoll-Rozada, J., Calisto, B.M.
• Funding Organization(s): Fundacao para a Ciencia e a Tecnologia

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.221 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

Starting Model: experimental

Literature

Synthesis and evaluation of peptidic thrombin inhibitors bearing acid-stable sulfotyrosine analogues.

Dowman, L.J., Agten, S.M., Ripoll-Rozada, J., Calisto, B.M., Pereira, P.J.B., Payne, R.J.

(2021) Chem Commun (Camb) 57: 10923-10926

• PubMed: 34596182 
• DOI: https://doi.org/10.1039/d1cc04742f
• Primary Citation of Related Structures:  
  7PHX


• PubMed Abstract: 
  

  Tyrosine sulfation is an important post-translational modification of peptides and proteins which underpins and modulates many protein-protein interactions. In order to overcome the inherent instability of the native modification, we report the synthesis of two sulfonate analogues and their incorporation into two thrombin-inhibiting sulfopeptides. The effective mimicry of these sulfonate analogues for native sulfotyrosine was validated in the context of their thrombin inhibitory activity and binding mode, as determined by X-ray crystallography.

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Organizational Affiliation: 

School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia. [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 37.65 kDa 
• Atom Count: 2,590 
• Modelled Residue Count: 300 
• Deposited Residue Count: 327 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin light chain	A [auth L]	36	Homo sapiens	Mutation(s): 0  EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin heavy chain	B [auth H]	259	Homo sapiens	Mutation(s): 0  EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734 GTEx:  ENSG00000180210
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P00734-1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tsetse thrombin inhibitor	C [auth I]	32	Glossina morsitans morsitans	Mutation(s): 2
UniProt
Find proteins for O97373 (Glossina morsitans morsitans) Explore O97373  Go to UniProtKB:  O97373

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
NA	E [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SMF	C [auth I]	L-PEPTIDE LINKING	C10 H13 N O5 S		PHE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.221 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.15785/SBGRID/846

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.7	α = 90
b = 80.788	β = 90
c = 85.891	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-10-06 
Deposition Author(s): Pereira, P.J.B., Ripoll-Rozada, J., Calisto, B.M.

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Funding Organization	Location	Grant Number
Fundacao para a Ciencia e a Tecnologia	Portugal	PTDC/BIA-BQM/2494/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	DL 57/2016/CP1355/CT0011

Revision History  

• Version 1.0: 2021-10-06
  Type: Initial release
  
• Version 1.1: 2021-10-13
  Changes: Data collection, Database references
• Version 1.2: 2021-10-27
  Changes: Data collection, Database references
• Version 1.3: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary