3U9A

Human Thrombin In Complex With MI330

• PDB DOI: https://doi.org/10.2210/pdb3U9A/pdb

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


• Deposited: 2011-10-18 Released: 2012-10-24 
• Deposition Author(s): Biela, A., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.196 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 

Starting Model: experimental

Literature

Thrombin Inhibition

Biela, A., Sielaff, F., Heine, A., Steinmetzer, T., Klebe, G.

To be published.

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: 36.79 kDa 
• Atom Count: 2,731 
• Modelled Residue Count: 290 
• Deposited Residue Count: 308 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin Light Chain	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
Thrombin Heavy Chain	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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P00734-1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hirudin variant-2	C [auth I]	13	Hirudo medicinalis	Mutation(s): 0
UniProt
Find proteins for P09945 (Hirudo medicinalis) Explore P09945  Go to UniProtKB:  P09945

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S33	E [auth H]	(2S)-N-[[2-(aminomethyl)-5-chloranyl-phenyl]methyl]-1-[(2S)-2-[(3-chloranyl-4-methoxy-phenyl)sulfonylamino]-4-[(4-cyanophenyl)methylamino]-4-oxidanylidene-butanoyl]pyrrolidine-2-carboxamide C32 H34 Cl2 N6 O6 S MSHHPYQVXLZTQG-NSOVKSMOSA-N
NAG	D [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4	H	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	F [auth H], G [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	I [auth H], J [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000887 (S33)	E [auth H]	(2S)-N-[[2-(AMINOMETHYL)-5-CHLORANYL-PHENYL]METHYL]-1-[(2S)-2-[(3-CHLORANYL-4-METHOXY-PHENYL)SULFONYLAMINO]-4-[(4-CYANOPHENYL)METHYLAMINO]-4-OXIDANYLIDENE-BUTANOYL]PYRROLIDINE-2-CARBOXAMIDE	Peptide-like / Thrombin inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.196 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.9	α = 90
b = 71.2	β = 100.1
c = 72.6	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-24 
Deposition Author(s): Biela, A., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2012-10-24
  Type: Initial release
  
• Version 1.1: 2012-12-12
  Changes: Other
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2023-12-06
  Changes: Data collection
• Version 1.5: 2024-10-30
  Changes: Structure summary