8WK1

Bovine trypsin in complex with Durio zibethinus trypsin inhibitor DzTI-4

PDB DOI: https://doi.org/10.2210/pdb8WK1/pdb

Classification: PLANT PROTEIN
Organism(s): Bos taurus, Durio zibethinus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-09-26 Released: 2024-10-02
Deposition Author(s): Deentanya, P., Wangkanont, K.
Funding Organization(s): National Research Council of Thailand (NRCT), Chulalongkorn University

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.224
R-Value Work: 0.177
R-Value Observed: 0.180

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Bovine trypsin in complex with Durio zibethinus trypsin inhibitor DzTI-4

Deentanya, P., Wangkanont, K.

To be published.

Macromolecule Content

Total Structure Weight: 91.57 kDa
Atom Count: 6,807
Modelled Residue Count: 811
Deposited Residue Count: 834
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cationic trypsin	A, C	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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
21 kDa seed protein-like	B, D	194	Durio zibethinus	Mutation(s): 0 Gene Names: LOC111287540
UniProt
Find proteins for A0A6P5Y0F4 (Durio zibethinus) Explore A0A6P5Y0F4 Go to UniProtKB: A0A6P5Y0F4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6P5Y0F4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain T [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain T [auth D] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain T [auth D]	E [auth A], K [auth B], L [auth B], T [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain T [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain M [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain Q [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain Q [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain Q [auth C]	F [auth A] G [auth A] H [auth A] J [auth B] M [auth B] F [auth A], G [auth A], H [auth A], J [auth B], M [auth B], N [auth C], O [auth C], Q [auth C], R [auth D], U [auth D], V [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain U [auth D] Focus chain V [auth D]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain P [auth C] SDF format, chain S [auth D] MOL2 format, chain I [auth A] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] mmCIF format, chain I [auth A] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D]	I [auth A], P [auth C], S [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain P [auth C] Focus chain S [auth D] Interactions & Density Focus chain I [auth A] Focus chain P [auth C] Focus chain S [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.224
R-Value Work: 0.177
R-Value Observed: 0.180
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.473	α = 90
b = 72.055	β = 90
c = 147.495	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-10-02

Deposition Author(s):

Deentanya, P.

Wangkanont, K.

Funding Organization	Location	Grant Number
National Research Council of Thailand (NRCT)	Thailand	N42A650270
Chulalongkorn University	Thailand	RES_65_389_23_039
Chulalongkorn University	Thailand	CU_GR_62_28_23_10