4AYV

Human thrombin - inhibitor complex

• PDB DOI: https://doi.org/10.2210/pdb4AYV/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Homo sapiens, Hirudo medicinalis
• Mutation(s): No 


• Deposited: 2012-06-22 Released: 2012-08-15 
• Deposition Author(s): Banner, D.W., D'Arcy, A., Winkler, F.K., Hilpert, K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.192 
• R-Value Work: 0.141 
• R-Value Observed: 0.143 

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: 35.35 kDa 
• Atom Count: 2,551 
• Modelled Residue Count: 298 
• Deposited Residue Count: 298 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THROMBIN LIGHT CHAIN	A	30	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	257	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	Sequence Length	Organism	Details	Image
HIRUDIN-3A'	C [auth D]	11	Hirudo medicinalis	Mutation(s): 0
UniProt
Find proteins for P28508 (Hirudo medicinalis) Explore P28508  Go to UniProtKB:  P28508

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9MQ	D [auth B]	{Benzyl-[(S)-3-[((S)-1-carbamimidoyl-piperidin-3-ylmethyl)-carbamoyl]-2-(naphthalene-2-sulfonylamino)-propionyl]-amino}-acetic acid C30 H36 N6 O6 S ZWJYDBRLGHLMKT-NVQXNPDNSA-N
NAG	E [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
NA	F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
9MQ	PDBBind:  4AYV	Ki: 0.68 (nM) from 1 assay(s)
	BindingDB:  4AYV	Ki: 0.68 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.192 
• R-Value Work: 0.141 
• R-Value Observed: 0.143 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.8	α = 90
b = 90.8	β = 90
c = 132.5	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-15 
Deposition Author(s): Banner, D.W., D'Arcy, A., Winkler, F.K., Hilpert, K.

Revision History  

• Version 1.0: 2012-08-15
  Type: Initial release
  
• Version 1.1: 2013-08-07
  Changes: Other
• Version 1.2: 2017-06-28
  Changes: Data collection
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary