8ASE | pdb_00008ase

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 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.210 (DCC) 

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 
• Modeled 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 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.210 (DCC) 

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