4ABI | pdb_00004abi

Co-complex structure of bovine trypsin with a modified Bowman-Birk inhibitor (PtA)SFTI-1(1,14), that was 1,4-disubstituted with a 1,2,3- trizol to mimic a trans amide bond

PDB DOI: https://doi.org/10.2210/pdb4ABI/pdb

Classification: HYDROLASE/INHIBITOR
Organism(s): Bos taurus, synthetic construct
Mutation(s): No

Deposited: 2011-12-08 Released: 2012-03-07
Deposition Author(s): Schmelz, S., Empting, M., Tischler, M., Nasu, D., Heinz, D., Kolmar, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.220 (Depositor), 0.224 (DCC)
R-Value Work:
0.190 (Depositor), 0.193 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Braces for the Peptide Backbone: Insights Into Structure-Activity Relation-Ships of Protease Inhibitor Mimics with Locked Amide Conformations

Tischler, M., Nasu, D., Empting, M., Schmelz, S., Heinz, D., Rottmann, P., Kolmar, H., Buntkowsky, G., Tietze, D., Avrutina, O.

(2012) Angew Chem Int Ed Engl 51: 3708

PubMed: 22374650 Search on PubMed
DOI: https://doi.org/10.1002/anie.201108983
Primary Citation Related Structures:
4ABI, 4ABJ

Organizational Affiliation

Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Petersenstrasse 22, 64287 Darmstadt, Germany.

Macromolecule Content

Total Structure Weight: 25.95 kDa
Atom Count: 2,201
Modeled Residue Count: 234
Deposited Residue Count: 236
Unique protein chains: 2

Macromolecules

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| 3D Structure

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

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PTA-SFTI INHIBITOR	B	13	synthetic construct	Mutation(s): 0
UniProt
Find proteins for Q4GWU5 (Helianthus annuus) Explore Q4GWU5 Go to UniProtKB: Q4GWU5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4GWU5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A]	N [auth A], O [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain N [auth A] Focus chain O [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]
DMF Query on DMF Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A]	DIMETHYLFORMAMIDE C₃ H₇ N O ZMXDDKWLCZADIW-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
CA Query on CA 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]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000842 Query on PRD_000842	B	PTA-SFTI INHIBITOR	Peptide-like / Inhibitor		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.220 (Depositor), 0.224 (DCC)
R-Value Work: 0.190 (Depositor), 0.193 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.1	α = 90
b = 63.2	β = 90
c = 69.9	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
DENZO	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-03-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-03-07
Type: Initial release
Version 1.1: 2012-04-18
Changes: Other
Version 1.2: 2012-05-16
Changes: Other
Version 1.3: 2012-11-14
Changes: Database references
Version 1.4: 2012-11-30
Changes: Other
Version 1.5: 2017-06-28
Changes: Data collection
Version 2.0: 2023-11-15
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other
Version 2.1: 2023-12-20
Changes: Refinement description
Version 2.2: 2024-11-13
Changes: Structure summary