7QIQ | pdb_00007qiq

CRYSTAL STRUCTURE OF THE P1 aminobutanoic acid (ABU) BPTI MUTANT- BOVINE CHYMOTRYPSIN COMPLEX

PDB DOI: https://doi.org/10.2210/pdb7QIQ/pdb

Classification: HYDROLASE
Organism(s): Bos taurus
Mutation(s): Yes

Deposited: 2021-12-15 Released: 2022-03-09
Deposition Author(s): Dimos, N., Leppkes, J., Koksch, B., Wahl, M.C., Loll, B.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.188 (Depositor), 0.186 (DCC)
R-Value Work:
0.161 (Depositor), 0.160 (DCC)
R-Value Observed:
0.162 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Fluorine-induced polarity increases inhibitory activity of BPTI towards chymotrypsin.

Leppkes, J., Dimos, N., Loll, B., Hohmann, T., Dyrks, M., Wieseke, A., Keller, B.G., Koksch, B.

(2022) RSC Chem Biol 3: 773-782

PubMed: 35755190 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1039/d2cb00018k
Primary Citation Related Structures:
7QIQ, 7QIR, 7QIS, 7QIT

PubMed Abstract:
Substituting the P ₁ position in bovine pancreatic trypsin inhibitor (BPTI) is known to heavily influence its inhibitory activity towards serine proteases. Side-chain fluorinated aliphatic amino acids have been shown to alter numerous properties of peptides and proteins and thus are of interest in the context of BPTI. In our study, we systematically investigated the site-specific incorporation of non-canonical amino acids into BPTI by microwave-assisted solid-phase peptide synthesis (SPPS). Inhibitor activity of the variants was tested towards the serine protease α-chymotrypsin. We observed enhanced inhibition of two fluorinated BPTIs compared to wild type and hydrocarbon variants. To further investigate the complexes, we performed X-ray structure analysis. Our findings underline the power fluorine offers as a tool in protein engineering to beneficially alter the effects on phenomena as protein-protein interactions.

Organizational Affiliation

Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin Arnimallee 20 14195 Berlin Germany beate.koksch@fu-berlin.de.

Macromolecule Content

Total Structure Weight: 67.6 kDa
Atom Count: 5,464
Modeled Residue Count: 594
Deposited Residue Count: 598
Unique protein chains: 4

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chymotrypsin A chain A	A, E	13	Bos taurus	Mutation(s): 0 EC: 3.4.21.1
UniProt
Find proteins for P00766 (Bos taurus) Explore P00766 Go to UniProtKB: P00766
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00766
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Chymotrypsin A chain B	B, F	131	Bos taurus	Mutation(s): 0 EC: 3.4.21.1
UniProt
Find proteins for P00766 (Bos taurus) Explore P00766 Go to UniProtKB: P00766
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00766
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Chymotrypsin A chain C	C, G	97	Bos taurus	Mutation(s): 0 EC: 3.4.21.1
UniProt
Find proteins for P00766 (Bos taurus) Explore P00766 Go to UniProtKB: P00766
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00766
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Pancreatic trypsin inhibitor	D, H	58	Bos taurus	Mutation(s): 1
UniProt
Find proteins for P00974 (Bos taurus) Explore P00974 Go to UniProtKB: P00974
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00974
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain O [auth B] SDF format, chain OA [auth F] SDF format, chain P [auth B] SDF format, chain VA [auth G] SDF format, chain WA [auth G] SDF format, chain ZA [auth H] SDF format, chain PA [auth F] SDF format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain VA [auth G] MOL2 format, chain WA [auth G] MOL2 format, chain ZA [auth H] MOL2 format, chain PA [auth F] MOL2 format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain GA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain IA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain VA [auth G] mmCIF format, chain WA [auth G] mmCIF format, chain ZA [auth H] mmCIF format, chain PA [auth F] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] CA [auth C] GA [auth D] HA [auth D] AA [auth C], BA [auth C], CA [auth C], GA [auth D], HA [auth D], IA [auth D], JA [auth D], KA [auth D], O [auth B], OA [auth F], P [auth B], PA [auth F], VA [auth G], WA [auth G], ZA [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain O [auth B] Focus chain OA [auth F] Focus chain P [auth B] Focus chain PA [auth F] Focus chain VA [auth G] Focus chain WA [auth G] Focus chain ZA [auth H] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain O [auth B] Focus chain OA [auth F] Focus chain P [auth B] Focus chain PA [auth F] Focus chain VA [auth G] Focus chain WA [auth G] Focus chain ZA [auth H]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain LA [auth F] SDF format, chain M [auth B] SDF format, chain MA [auth F] SDF format, chain N [auth B] SDF format, chain NA [auth F] SDF format, chain Q [auth C] SDF format, chain QA [auth G] SDF format, chain R [auth C] SDF format, chain RA [auth G] SDF format, chain S [auth C] SDF format, chain SA [auth G] SDF format, chain TA [auth G] SDF format, chain UA [auth G] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain XA [auth H] SDF format, chain Y [auth C] SDF format, chain YA [auth H] SDF format, chain Z [auth C] SDF format, chain U [auth C] SDF format, chain T [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain LA [auth F] MOL2 format, chain M [auth B] MOL2 format, chain MA [auth F] MOL2 format, chain N [auth B] MOL2 format, chain NA [auth F] MOL2 format, chain Q [auth C] MOL2 format, chain QA [auth G] MOL2 format, chain R [auth C] MOL2 format, chain RA [auth G] MOL2 format, chain S [auth C] MOL2 format, chain SA [auth G] MOL2 format, chain TA [auth G] MOL2 format, chain UA [auth G] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth H] MOL2 format, chain Y [auth C] MOL2 format, chain YA [auth H] MOL2 format, chain Z [auth C] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain LA [auth F] mmCIF format, chain M [auth B] mmCIF format, chain MA [auth F] mmCIF format, chain N [auth B] mmCIF format, chain NA [auth F] mmCIF format, chain Q [auth C] mmCIF format, chain QA [auth G] mmCIF format, chain R [auth C] mmCIF format, chain RA [auth G] mmCIF format, chain S [auth C] mmCIF format, chain SA [auth G] mmCIF format, chain TA [auth G] mmCIF format, chain UA [auth G] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain XA [auth H] mmCIF format, chain Y [auth C] mmCIF format, chain YA [auth H] mmCIF format, chain Z [auth C] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C]	DA [auth D] EA [auth D] FA [auth D] I [auth B] J [auth B] DA [auth D], EA [auth D], FA [auth D], I [auth B], J [auth B], K [auth B], L [auth B], LA [auth F], M [auth B], MA [auth F], N [auth B], NA [auth F], Q [auth C], QA [auth G], R [auth C], RA [auth G], S [auth C], SA [auth G], T [auth C], TA [auth G], U [auth C], UA [auth G], V [auth C], W [auth C], X [auth C], XA [auth H], Y [auth C], YA [auth H], Z [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain LA [auth F] Focus chain M [auth B] Focus chain MA [auth F] Focus chain N [auth B] Focus chain NA [auth F] Focus chain Q [auth C] Focus chain QA [auth G] Focus chain R [auth C] Focus chain RA [auth G] Focus chain S [auth C] Focus chain SA [auth G] Focus chain T [auth C] Focus chain TA [auth G] Focus chain U [auth C] Focus chain UA [auth G] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain XA [auth H] Focus chain Y [auth C] Focus chain YA [auth H] Focus chain Z [auth C] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain LA [auth F] Focus chain M [auth B] Focus chain MA [auth F] Focus chain N [auth B] Focus chain NA [auth F] Focus chain Q [auth C] Focus chain QA [auth G] Focus chain R [auth C] Focus chain RA [auth G] Focus chain S [auth C] Focus chain SA [auth G] Focus chain T [auth C] Focus chain TA [auth G] Focus chain U [auth C] Focus chain UA [auth G] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain XA [auth H] Focus chain Y [auth C] Focus chain YA [auth H] Focus chain Z [auth C]