Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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: 35.17 kDa 
• Atom Count: 2536 
• Residue Count: 289 
• Unique protein chains: 3

3BIV

Human thrombin-in complex with UB-THR11

• DOI: 10.2210/pdb3BIV/pdb

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


• Deposited: 2007-12-01 Released: 2007-12-25 
• Deposition Author(s): Gerlach, C., Smolinski, M., Steuber, H., Sotriffer, C.A., Heine, A., Hangauer, D.G., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.264 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 

Literature

Thermodynamic Inhibition Profile of a Cyclopentyl and a Cyclohexyl Derivative towards Thrombin: The Same but for Different Reasons

Gerlach, C., Smolinski, M., Steuber, H., Sotriffer, C.A., Heine, A., Hangauer, D.G., Klebe, G.

(2007) Angew Chem Int Ed Engl 46: 8511-8514

• PubMed: 17902081 
• DOI: 10.1002/anie.200701169
• Primary Citation of Related Structures:  
  3BIU, 3BIV

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin light chain	L	29	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin heavy chain	H	257	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hirudin	I	12	Hirudo medicinalis	Mutation(s): 0
Find proteins for P09945 (Hirudo medicinalis) Explore P09945  Go to UniProtKB:  P09945

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
11U	H	(S)-N-(4-carbamimidoylbenzyl)-1-(2-(cyclohexylamino)ethanoyl)pyrrolidine-2-carboxamide C21 H31 N5 O2 RYKFVFFOIYLADT-SFHVURJKSA-N
NAG	H	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS	I	L-PEPTIDE LINKING	C9 H11 N O6 S		TYR

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
11U	Ki:  56100   nM  BindingDB
11U	Ki:  68000   nM  BindingDB

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000587 (11U)	H	(S)-N-(4-carbamimidoylbenzyl)-1-(2-(cyclohexylamino)ethanoyl)pyrrolidine-2-carboxamide	Peptide-like /  Thrombin inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.264 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.7	α = 90
b = 71.5	β = 100.9
c = 72.8	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNS	refinement
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-12-01 
• Released Date: 2007-12-25 
Deposition Author(s): Gerlach, C., Smolinski, M., Steuber, H., Sotriffer, C.A., Heine, A., Hangauer, D.G., Klebe, G.

Revision History 

• Version 1.0: 2007-12-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• 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