1TX7

Bovine Trypsin complexed with p-amidinophenylmethylphosphinic acid (AMPA)

PDB DOI: https://doi.org/10.2210/pdb1TX7/pdb

Classification: HYDROLASE
Organism(s): Bos taurus
Mutation(s): No

Deposited: 2004-07-02 Released: 2005-09-20
Deposition Author(s): Cui, J., Marankan, F., Fu, W., Crich, D., Mesecar, A., Johnson, M.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.229 (Depositor)
R-Value Work:
0.183 (Depositor), 0.173 (DCC)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

An oxyanion-hole selective serine protease inhibitor in complex with trypsin.

Cui, J., Marankan, F., Fu, W., Crich, D., Mesecar, A., Johnson, M.E.

(2002) Bioorg Med Chem 10: 41-46

PubMed: 11738605 Search on PubMed
DOI: https://doi.org/10.1016/s0968-0896(01)00259-0
Primary Citation of Related Structures:
1TX7

PubMed Abstract:
p-amidinophenylmethylphosphinic acid (AMPA) was designed, synthesized and crystallized in complex with trypsin to study interactions with the oxyanion hole at the S1 site. In comparison to benzamidine, AMPA shows improved activity, which the crystal structure demonstrates to result from hydrogen bonds between the negatively charged phosphinic acid group and the catalytic residues at the oxyanion hole.

Organizational Affiliation

Center for Pharmaceutical Biotechnology, College of Pharmacy, University of Illinois at Chicago, 900 S. Ashland Avenue, M/C 870, Chicago, IL 60607-7173, USA.

Macromolecule Content

Total Structure Weight: 23.56 kDa
Atom Count: 1,735
Modelled Residue Count: 223
Deposited Residue Count: 223
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trypsinogen	A	223	Bos taurus	Mutation(s): 0 EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus) Explore P00760 Go to UniProtKB: P00760
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00760
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4CM Query on 4CM Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(4-CARBAMIMIDOYLPHENYL)-METHYL-PHOSPHINIC ACID C₈ H₁₁ N₂ O₂ P CVABPMXIKVDCLF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.229 (Depositor)
R-Value Work: 0.183 (Depositor), 0.173 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.87	α = 90
b = 58.44	β = 90
c = 67.52	γ = 90

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-09-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-09-20
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-04-04
Changes: Data collection
Version 1.4: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary