1UHB | pdb_00001uhb

Crystal structure of porcine alpha trypsin bound with auto catalyticaly produced native peptide at 2.15 A resolution

PDB DOI: https://doi.org/10.2210/pdb1UHB/pdb

Classification: HYDROLASE
Organism(s): Sus scrofa
Mutation(s): No

Deposited: 2003-06-27 Released: 2004-07-27
Deposition Author(s): Pattabhi, V., Syed Ibrahim, B., Shamaladevi, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.228 (Depositor), 0.253 (DCC)
R-Value Work:
0.193 (Depositor), 0.192 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Trypsin activity reduced by an autocatalytically produced nonapeptide.

Ibrahim, B.S., Shamaladevi, N., Pattabhi, V.

(2004) J Biomol Struct Dyn 21: 737-744

PubMed: 15106996 Search on PubMed
DOI: https://doi.org/10.1080/07391102.2004.10506964
Primary Citation Related Structures:
1UHB

PubMed Abstract:
Trypsin, a serine protease enzyme plays a pivotal role in digestion and is autocatalytic. The crystal structure of a complex formed between porcine trypsin and an auto catalytically produced peptide is reported here. This complex shows a reduction in enzyme activity as compared to native beta-trypsin. The nonapeptide has a lysine, which is recognized by Asp 189 at the specificity pocket. The auto catalytically produced native nonapeptide is bound at the active site cleft like other trypsin inhibitors but the important interactions with the oxyanion hole are absent. The peptide covers only a part of the active site cleft and hence the enzyme activity is reduced rather than being inhibited.

Organizational Affiliation

Department of Crystallography and Biophysics, University of Madras, Guindy Campus, Guindy, Chennai-600025, India.

Macromolecule Content

Total Structure Weight: 24.51 kDa
Atom Count: 1,856
Modeled Residue Count: 232
Deposited Residue Count: 232
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trypsin	A	125	Sus scrofa	Mutation(s): 0 EC: 3.4.21.4
UniProt
Find proteins for P00761 (Sus scrofa) Explore P00761 Go to UniProtKB: P00761
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00761
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Trypsin	B	98	Sus scrofa	Mutation(s): 0 EC: 3.4.21.4
UniProt
Find proteins for P00761 (Sus scrofa) Explore P00761 Go to UniProtKB: P00761
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00761
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
9-mer peptide from Trypsin	C [auth P]	9	Sus scrofa	Mutation(s): 0 EC: 3.4.21.4
UniProt
Find proteins for P00761 (Sus scrofa) Explore P00761 Go to UniProtKB: P00761
Entity Groups
UniProt Group	P00761
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth P] MOL2 format, chain E [auth P] mmCIF format, chain E [auth P]	E [auth P]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth P] Interactions & Density Focus chain E [auth P]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.228 (Depositor), 0.253 (DCC)
R-Value Work: 0.193 (Depositor), 0.192 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.945	α = 90
b = 53.921	β = 90
c = 77.245	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
DENZO	data reduction
CNS	refinement
REFMAC	refinement
SCALEPACK	data scaling
CNS	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2004-07-27

Deposition Author(s):

Pattabhi, V.

Syed Ibrahim, B.

Shamaladevi, N.

Revision History (Full details and data files)

Version 1.0: 2004-07-27
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-04
Changes: Refinement description
Version 1.4: 2019-11-06
Changes: Data collection, Database references
Version 1.5: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.6: 2024-11-13
Changes: Structure summary