9EYG | pdb_00009eyg

Structure of Tannerella forsythia endopeptidase O (TfPepO)

PDB DOI: https://doi.org/10.2210/pdb9EYG/pdb

Classification: HYDROLASE
Organism(s): Tannerella forsythia
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-04-09 Released: 2025-10-29
Deposition Author(s): Zak, K.M., Grudnik, P., Waligorska, I., Ksiazek, M.
Funding Organization(s): Polish National Science Centre

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.223 (Depositor), 0.223 (DCC)
R-Value Work:
0.194 (Depositor), 0.194 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structure of Tannerella forsythia endopeptidase O (TfPepO)

Zak, K., Waligorska, I., Ksiazek, M.

To be published.

Macromolecule Content

Total Structure Weight: 151.88 kDa
Atom Count: 11,540
Modeled Residue Count: 1,299
Deposited Residue Count: 1,304
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase family M13	A, B	652	Tannerella forsythia	Mutation(s): 0 Gene Names: BFO_0011 EC: 3.4.24
UniProt
Find proteins for G8UQE9 (Tannerella forsythia (strain ATCC 43037 / JCM 10827 / CCUG 21028 A / KCTC 5666 / FDC 338)) Explore G8UQE9 Go to UniProtKB: G8UQE9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G8UQE9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A]	S [auth A], T [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain S [auth A] Focus chain T [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain F [auth A] SDF format, chain D [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A]	D [auth A], F [auth A], X [auth B], Y [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain X [auth B] Focus chain Y [auth B]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain GA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain GA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain GA [auth B]	GA [auth B], O [auth A], P [auth A], Q [auth A], R [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain GA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain GA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain IA [auth B] SDF format, chain HA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain HA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain HA [auth B]	HA [auth B], IA [auth B], U [auth A], V [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain HA [auth B] Focus chain IA [auth B] Focus chain U [auth A] Focus chain V [auth A] Interactions & Density Focus chain HA [auth B] Focus chain IA [auth B] Focus chain U [auth A] Focus chain V [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain DA [auth B] SDF format, chain FA [auth B] SDF format, chain G [auth A] SDF format, chain K [auth A] SDF format, chain W [auth A] SDF format, chain Z [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain EA [auth B] SDF format, chain E [auth A] SDF format, chain CA [auth B] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain C [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain K [auth A] MOL2 format, chain W [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain C [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain K [auth A] mmCIF format, chain W [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] C [auth A] CA [auth B] DA [auth B] AA [auth B], BA [auth B], C [auth A], CA [auth B], DA [auth B], E [auth A], EA [auth B], FA [auth B], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], W [auth A], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain C [auth A] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain FA [auth B] 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] Focus chain M [auth A] Focus chain N [auth A] Focus chain W [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain C [auth A] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain FA [auth B] 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] Focus chain M [auth A] Focus chain N [auth A] Focus chain W [auth A] Focus chain Z [auth B]