4DII

X-ray structure of the complex between human alpha thrombin and thrombin binding aptamer in the presence of potassium ions

• PDB DOI: https://doi.org/10.2210/pdb4DII/pdb
• NAKB: 4DII

• Classification: HYDROLASE/HYDROLASE INHIBITOR/DNA
• Organism(s): Homo sapiens, synthetic construct
• Mutation(s): No 


• Deposited: 2012-01-31 Released: 2012-07-18 
• Deposition Author(s): Russo Krauss, I., Merlino, A., Mazzarella, L., Sica, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.226 
• R-Value Work: 0.174 
• R-Value Observed: 0.195 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 39.56 kDa 
• Atom Count: 2,814 
• Modelled Residue Count: 292 
• Deposited Residue Count: 310 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	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
Prothrombin	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

Entity ID: 3
Molecule	Chains	Length	Organism	Image
Thrombin binding aptamer	C [auth D]	15	synthetic construct

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0G6	E [auth H]	D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide C21 H34 Cl N6 O3 DVFLYEYCMMLBTQ-VSZNYVQBSA-O
NAG	F [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	D [auth L], H	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
K	K [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	I [auth H], J [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	G [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000020 (0G6)	E [auth H]	D-Phe-Pro-Arg-CH2Cl	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.226 
• R-Value Work: 0.174 
• R-Value Observed: 0.195 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.369	α = 68.97
b = 45.299	β = 86.11
c = 51.519	γ = 69.66

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASES	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-18 
Deposition Author(s): Russo Krauss, I., Merlino, A., Mazzarella, L., Sica, F.

Revision History  

• Version 1.0: 2012-07-18
  Type: Initial release
  
• Version 1.1: 2012-09-26
  Changes: Database references
• Version 1.2: 2013-02-27
  Changes: Other
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary