9AWM | pdb_00009awm

Crystal structure of trypsin at 225 Kelvin with benzamidine (Triplicate)

PDB DOI: https://doi.org/10.2210/pdb9AWM/pdb

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

Deposited: 2024-03-05 Released: 2025-03-12
Deposition Author(s): Lima, L.M.T.R., de Sa Ribeiro, F.
Funding Organization(s): Brazilian National Council for Scientific and Technological Development (CNPq)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.219 (Depositor), 0.219 (DCC)
R-Value Work:
0.191 (Depositor), 0.191 (DCC)

Starting Model: experimental
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This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of trypsin at 225 Kelvin with benzamidine (Triplicate)

Lima, L.M.T.R., de Sa Ribeiro, F.

To be published.

Macromolecule Content

Total Structure Weight: 23.48 kDa
Atom Count: 1,832
Modeled Residue Count: 223
Deposited Residue Count: 223
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cationic trypsin	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00760
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BEN Query on BEN 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]	BENZAMIDINE C₇ H₈ N₂ PXXJHWLDUBFPOL-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: 1.50 Å
R-Value Free: 0.219 (Depositor), 0.219 (DCC)
R-Value Work: 0.191 (Depositor), 0.191 (DCC)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.866	α = 90
b = 57.041	β = 90
c = 66.72	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-03-12

Deposition Author(s):

de Sa Ribeiro, F.

Funding Organization	Location	Grant Number
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	--

Revision History (Full details and data files)

Version 1.0: 2025-03-12
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.