9SRH | pdb_00009srh

helical form of Polybia-CP

PDB DOI: https://doi.org/10.2210/pdb9SRH/pdb

Classification: ANTIMICROBIAL PROTEIN
Organism(s): Polybia paulista
Mutation(s): Yes

Deposited: 2025-09-24 Released: 2026-10-07
Deposition Author(s): Bloch, Y., Golubev, A., Landau, M.
Funding Organization(s): European Research Council (ERC), H2020 Marie Curie Actions of the European Commission, Israel Science Foundation, Volkswagen Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.13 Å
R-Value Free:
0.123 (Depositor), 0.121 (DCC)
R-Value Work:
0.116 (Depositor), 0.116 (DCC)
R-Value Observed:
0.116 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

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

Literature

A Fate Amenable To Change: Chameleon Characteristics of Antimicrobial Peptides from Wasp Venom and Frog Skin

Golubev, A., Bloch, Y., Strati, F., Pigozzi Cali, M., Gustavsson, E., Landau, M.

To be published.

Macromolecule Content

Total Structure Weight: 8.17 kDa
Atom Count: 714
Modeled Residue Count: 78
Deposited Residue Count: 78
Unique protein chains: 1

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polybia-CP	A [auth F] B [auth A] C [auth B] D [auth C] E [auth D] A [auth F], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E]	13	Polybia paulista	Mutation(s): 1
UniProt
Find proteins for P0C1R0 (Polybia paulista) Explore P0C1R0 Go to UniProtKB: P0C1R0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C1R0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TFA Query on TFA Download:Ideal Coordinates CCD File SDF format, chain G [auth F] MOL2 format, chain G [auth F] mmCIF format, chain G [auth F]	G [auth F]	trifluoroacetic acid C₂ H F₃ O₂ DTQVDTLACAAQTR-UHFFFAOYSA-N		Interactions Focus chain G [auth F] Interactions & Density Focus chain G [auth F]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth F] SDF format, chain I [auth F] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain H [auth F] MOL2 format, chain I [auth F] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain H [auth F] mmCIF format, chain I [auth F] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	H [auth F] I [auth F] J [auth A] K [auth A] L [auth A] H [auth F], I [auth F], J [auth A], K [auth A], L [auth A], M [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth F] Focus chain I [auth F] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain H [auth F] Focus chain I [auth F] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A]	N [auth A], O [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain N [auth A] Focus chain O [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.13 Å
R-Value Free: 0.123 (Depositor), 0.121 (DCC)
R-Value Work: 0.116 (Depositor), 0.116 (DCC)
R-Value Observed: 0.116 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.067	α = 90
b = 38.703	β = 101.98
c = 22.936	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
STARANISO	data scaling
Arcimboldo	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-07

Deposition Author(s):

Bloch, Y.

Golubev, A.

Landau, M.

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	101087140
H2020 Marie Curie Actions of the European Commission	European Union	945405
Israel Science Foundation	Israel	2111/20
Volkswagen Foundation	Germany	76251-4659/2022 (ZN 4042)