Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 25.29 kDa 
• Atom Count: 1815 
• Residue Count: 223 
• Unique protein chains: 1

1ZZZ

Trypsin inhibitors with rigid tripeptidyl aldehydes

• DOI: 10.2210/pdb1ZZZ/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 1998-06-02 Released: 1999-06-15 
• Deposition Author(s): Krishnan, R., Zhang, E., Hakansson, K., Arni, R.K., Tulinsky, A., Lim-Wilby, M.S.L., Levy, O.E., Semple, J.E., Brunck, T.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Work: 0.157 

Literature

Highly selective mechanism-based thrombin inhibitors: structures of thrombin and trypsin inhibited with rigid peptidyl aldehydes.

Krishnan, R., Zhang, E., Hakansson, K., Arni, R.K., Tulinsky, A., Lim-Wilby, M.S., Levy, O.E., Semple, J.E., Brunck, T.K.

(1998) Biochemistry 37: 12094-12103

• PubMed: 9724521 
• DOI: 10.1021/bi980840e
• Primary Citation of Related Structures:  
  1BB0, 1BA8, 1CA8, 1YYY, 1ZZZ


• PubMed Abstract: 
  

The crystal structures of three highly potent and selective low-molecular weight rigid peptidyl aldehyde inhibitors complexed with thrombin have been determined and refined to R values 0.152-0. 170 at 1.8-2.1 A resolution. Since the selectivity of two of the inhibitors was >1600 with respect to trypsin, the structures of trypsin-inhibited complexes of these inhibitors were also determined (R = 0.142-0.157 at 1.9-2.1 A resolution). The selectivity appears to reside in the inability of a benzenesulfonamide group to bind at the equivalent of the D-enantiomorphic S3 site of thrombin, which may be related to the lack of a 60-insertion loop in trypsin. All the inhibitors have a novel lactam moiety at the P3 position, while the two with greatest trypsin selectivity have a guanidinopiperidyl group at the P1 position that binds in the S1 specificity site. Differences in the binding constants of these inhibitors are correlated with their interactions with thrombin and trypsin. The kinetics of inhibition vary from slow to fast with thrombin and are fast in all cases with trypsin. The kinetics are examined in terms of the slow formation of a stable transition-state complex in a two-step mechanism. The structures of both thrombin and trypsin complexes show similar well-defined transition states in the S1 site and at the electrophilic carbon atom and Ser195OG. The trypsin structures, however, suggest that the first step in a two-step kinetic mechanism may involve formation of a weak transition-state complex, rather than binding dominated by the P2-P4 positions.

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Organizational Affiliation: 

Corvas International Inc., San Diego, California 92121, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRYPSIN	A	237	Bos taurus	Mutation(s): 0  EC: 3.4.21.4
Find proteins for P00760 (Bos taurus) Explore P00760  Go to UniProtKB:  P00760

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0IV	A	2-{(3S)-3-[(benzylsulfonyl)amino]-2-oxopiperidin-1-yl}-N-{(2S)-1-[(3R)-1-carbamimidoylpiperidin-3-yl]-3-oxopropan-2-yl}acetamide C23 H34 N6 O5 S DATYERRDSFNBDN-AABGKKOBSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000324 (0IV)	A	N-(benzylsulfonyl)-L-norvalyl-N-{(1R)-2-[(3R)-1-carbamimidoylpiperidin-3-yl]-1-formylethyl}glycinamide	Peptide-like /  Inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Work: 0.157 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.67	α = 90
b = 63.2	β = 90
c = 69.22	γ = 90

Software Package:

Software Name	Purpose
RIGAKU	data collection
RIGAKU	data reduction
X-PLOR	model building
PROLSQ	refinement
X-PLOR	refinement
RIGAKU	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-06-02 
• Released Date: 1999-06-15 
Deposition Author(s): Krishnan, R., Zhang, E., Hakansson, K., Arni, R.K., Tulinsky, A., Lim-Wilby, M.S.L., Levy, O.E., Semple, J.E., Brunck, T.K.

Revision History 

• Version 1.0: 1999-06-15
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other