8WKB

Durio zibethinus trypsin inhibitor DzTI-7

PDB DOI: https://doi.org/10.2210/pdb8WKB/pdb

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

Deposited: 2023-09-27 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: 2.35 Å
R-Value Free: 0.242
R-Value Work: 0.192
R-Value Observed: 0.195

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Durio zibethinus trypsin inhibitor DzTI-7

Deentanya, P., Wangkanont, K.

To be published.

Macromolecule Content

Total Structure Weight: 86.59 kDa
Atom Count: 6,188
Modelled Residue Count: 727
Deposited Residue Count: 772
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
21 kDa seed protein-like	A, B, C, D	193	Durio zibethinus	Mutation(s): 0 Gene Names: LOC111287850
UniProt
Find proteins for A0A6P5Y1F9 (Durio zibethinus) Explore A0A6P5Y1F9 Go to UniProtKB: A0A6P5Y1F9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6P5Y1F9
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.242
R-Value Work: 0.192
R-Value Observed: 0.195
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.242	α = 90
b = 102.68	β = 90
c = 116.922	γ = 90

Software Package:

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

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