9G0J | pdb_00009g0j

Structure of the PRO-PRO endopeptidase (PPEP-3) from Geobacillus thermodenitrificans

PDB DOI: https://doi.org/10.2210/pdb9G0J/pdb

Classification: HYDROLASE
Organism(s): Geobacillus thermodenitrificans NG80-2
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2024-07-08 Released: 2025-07-16
Deposition Author(s): Claushuis, B., Wojtalla, F., van Leeuwen, H., Corver, J., Baumann, U., Hensbergen, P.
Funding Organization(s): Netherlands Organisation for Scientific Research (NWO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.198 (Depositor), 0.199 (DCC)
R-Value Work:
0.173 (Depositor), 0.174 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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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

Structural analyses and substrate profiling of PPEP-3 provide new insights into the molecular basis of Pro-Pro endopeptidase specificity

Claushuis, B., Wojtalla, F., Papenhagen, L., Cordfunke, R.A., de Ru, A.H., van Leeuwen, H.C., Corver, J., Hensbergen, P.J., Baumann, U.

(2026) iScience 29: 114360

DOI: https://doi.org/10.1016/j.isci.2025.114360

Macromolecule Content

Total Structure Weight: 53.6 kDa
Atom Count: 3,731
Modeled Residue Count: 421
Deposited Residue Count: 460
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATLF-like domain-containing protein	A, B	230	Geobacillus thermodenitrificans NG80-2	Mutation(s): 0 Gene Names: GTNG_1672
UniProt
Find proteins for A4INY2 (Geobacillus thermodenitrificans (strain NG80-2)) Explore A4INY2 Go to UniProtKB: A4INY2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A4INY2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCN (Subject of Investigation/LOI) Query on BCN Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	D [auth A], H [auth B]	BICINE C₆ H₁₃ N O₄ FSVCELGFZIQNCK-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B], J [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]