8S1X

Crystal structure of Actinonin-bound PDF1 and the computationally designed DBAct553_1 protein binder

PDB DOI: https://doi.org/10.2210/pdb8S1X/pdb

Classification: DE NOVO PROTEIN
Organism(s): Pseudomonas aeruginosa, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-02-16 Released: 2024-10-30
Deposition Author(s): Marchand, A., Pacesa, M., Correia, B.E.
Funding Organization(s): European Research Council (ERC), Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.203
R-Value Work: 0.184
R-Value Observed: 0.185

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Targeting protein-ligand neosurface with a generalizable deep learning tool

Marchand, A., Buckley, S., Schneuing, A., Pacesa, M., Gainza, P., Elizarova, E., Neeser, R., Reymond, L., Georgeon, S., Schmidt, J., Correia, B.E.

(2025) Nature

DOI: https://doi.org/10.1038/s41586-024-08435-4

Macromolecule Content

Total Structure Weight: 28.78 kDa
Atom Count: 1,999
Modelled Residue Count: 228
Deposited Residue Count: 238
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A	168	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: def, PA0019 EC: 3.5.1.88
UniProt
Find proteins for Q9I7A8 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I7A8 Go to UniProtKB: Q9I7A8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9I7A8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DBAct553_1	B	70	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BB2 (Subject of Investigation/LOI) Query on BB2 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ACTINONIN C₁₉ H₃₅ N₃ O₅ XJLATMLVMSFZBN-VYDXJSESSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A]	M [auth A], N [auth A], O [auth A], P [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain Q [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain Q [auth B]	Q [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Interactions & Density Focus chain Q [auth B]