7FCN | pdb_00007fcn

Crystal strcture of PirA insecticidal protein from Photorhabdus akhurstii

PDB DOI: https://doi.org/10.2210/pdb7FCN/pdb

Classification: TOXIN
Organism(s): Photorhabdus akhurstii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-07-15 Released: 2022-07-20
Deposition Author(s): Prashar, A., Kumar, A., Kinkar, O., Hire, R.S., Makde, R.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.194 (Depositor), 0.195 (DCC)
R-Value Work:
0.166 (Depositor), 0.166 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structures of PirA and PirB toxins from Photorhabdus akhurstii subsp. akhurstii K-1

Prashar, A., Kinkar, O.U., Kumar, A., Hadapad, A.B., Makde, R.D., Hire, R.S.

(2023) Insect Biochem Mol Biol 162: 104014

DOI: https://doi.org/10.1016/j.ibmb.2023.104014

Macromolecule Content

Total Structure Weight: 54.16 kDa
Atom Count: 3,757
Modeled Residue Count: 400
Deposited Residue Count: 472
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insecticidal protein	A, B, C, D	118	Photorhabdus akhurstii	Mutation(s): 0 Gene Names: pirA
UniProt
Find proteins for G5DBH3 (Photorhabdus akhurstii) Explore G5DBH3 Go to UniProtKB: G5DBH3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G5DBH3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG6 Query on PG6 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C₁₂ H₂₆ O₆ DMDPGPKXQDIQQG-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B]	AA [auth C], L [auth B], M [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain AA [auth C] Focus chain L [auth B] Focus chain M [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B]	J [auth B], K [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain J [auth B] Focus chain K [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain X [auth B] SDF format, chain I [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain X [auth B] MOL2 format, chain I [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain X [auth B] mmCIF format, chain I [auth A]	I [auth A] V [auth B] W [auth B] X [auth B] Y [auth B] I [auth A], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain I [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain GA [auth D] SDF format, chain JA [auth D] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain IA [auth D] SDF format, chain HA [auth D] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain FA [auth D] SDF format, chain F [auth A] SDF format, chain EA [auth C] SDF format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain IA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain GA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain IA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain BA [auth C]	BA [auth C] CA [auth C] DA [auth C] EA [auth C] F [auth A] BA [auth C], CA [auth C], DA [auth C], EA [auth C], F [auth A], FA [auth D], G [auth A], GA [auth D], H [auth A], HA [auth D], IA [auth D], JA [auth D], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]