8ASE

Crystal structure of Thrombin in complex with macrocycle T3

• PDB DOI: https://doi.org/10.2210/pdb8ASE/pdb

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


• Deposited: 2022-08-19 Released: 2023-11-29 
• Deposition Author(s): Chinellato, M., Angelini, A., Nielsen, A., Heinis, C., Cendron, L.
• Funding Organization(s): Italian Ministry of Education

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.250 
• R-Value Work: 0.200 

Literature

Crystal structure of Thrombin in complex with optimized macrocycles T1 and T3

Nielsen, A., Chinellato, M., Cendron, L., Angelini, A., Heinis, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 69.76 kDa 
• Atom Count: 4,760 
• Modelled Residue Count: 562 
• Deposited Residue Count: 590 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin light chain	A [auth L], C [auth A]	36	Homo sapiens	Mutation(s): 0  Gene Names: F2 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], D [auth B]	259	Homo sapiens	Mutation(s): 0  Gene Names: F2 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

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth C]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NWR	F [auth H], H [auth B]	(8~{S},14~{S},18~{E})-8-[(4-chlorophenyl)methyl]-3,21-dithia-7,10,16-triazatricyclo[21.2.2.1^{10,14}]octacosa-1(26),18,23(27),24-tetraene-6,9,15-trione C30 H36 Cl N3 O3 S2 PYZAWVLVOFYELK-DXKRRACBSA-N
NAG	J [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	G [auth H], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.250 
• R-Value Work: 0.200 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.201	α = 90
b = 120.311	β = 90
c = 128.808	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-29 
Deposition Author(s): Chinellato, M., Angelini, A., Nielsen, A., Heinis, C., Cendron, L.

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Funding Organization	Location	Grant Number
Italian Ministry of Education	Italy	--

Revision History  

• Version 1.0: 2023-11-29
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Structure summary