9QDI | pdb_00009qdi

Crystal structure of BF3526 peptidase from Bacteroides fragilis in complex with a peptide

PDB DOI: https://doi.org/10.2210/pdb9QDI/pdb

Classification: HYDROLASE
Organism(s): Bacteroides fragilis NCTC 9343, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-03-06 Released: 2025-07-16
Deposition Author(s): Martinez Gascuena, A., Marquez-Monino, M.A., Manzanares-Gomez, A., Aguillo-Urarte, M., Trastoy, B.
Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.213 (Depositor), 0.212 (DCC)
R-Value Work:
0.171 (Depositor), 0.171 (DCC)
R-Value Observed:
0.173 (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

Structural insights into IgA recognition by M64 peptidases

Marquez-Monino, M.A., Martinez Gascuena, A., Azzam, T., Persson, A., Manzanares-Gomez, A., Aguillo-Urarte, M., Brown, T.T., Montero, A., Lood, R., Naegali, A., Du, J.J., Connell, S.R., Sastre, D.E., Sundberg, E.J., Trastoy, B.

To be published.

Macromolecule Content

Total Structure Weight: 373.7 kDa
Atom Count: 27,337
Modeled Residue Count: 3,234
Deposited Residue Count: 3,288
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoprotein	A, B, C, D, E A, B, C, D, E, F, G, H	409	Bacteroides fragilis NCTC 9343	Mutation(s): 0 Gene Names: BF9343_3433
UniProt
Find proteins for Q5L9L3 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore Q5L9L3 Go to UniProtKB: Q5L9L3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5L9L3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Synthetic peptide SER-THR-PRO-PRO	I, J, K, L	4	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEZ Query on HEZ Download Ideal Coordinates CCD File SDF format, chain WA [auth G] MOL2 format, chain WA [auth G] mmCIF format, chain WA [auth G]	WA [auth G]	HEXANE-1,6-DIOL C₆ H₁₄ O₂ XXMIOPMDWAUFGU-UHFFFAOYSA-N		Interactions Focus chain WA [auth G] Interactions & Density Focus chain WA [auth G]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain IA [auth D] MOL2 format, chain IA [auth D] mmCIF format, chain IA [auth D]	IA [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain IA [auth D] Interactions & Density Focus chain IA [auth D]
BU1 Query on BU1 Download Ideal Coordinates CCD File SDF format, chain PA [auth E] MOL2 format, chain PA [auth E] mmCIF format, chain PA [auth E]	PA [auth E]	1,4-BUTANEDIOL C₄ H₁₀ O₂ WERYXYBDKMZEQL-UHFFFAOYSA-N		Interactions Focus chain PA [auth E] Interactions & Density Focus chain PA [auth E]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain EB [auth H] SDF format, chain FB [auth H] SDF format, chain KA [auth E] SDF format, chain LA [auth E] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain RA [auth F] SDF format, chain SA [auth F] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain YA [auth G] SDF format, chain ZA [auth G] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain EB [auth H] MOL2 format, chain FB [auth H] MOL2 format, chain KA [auth E] MOL2 format, chain LA [auth E] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain RA [auth F] MOL2 format, chain SA [auth F] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain YA [auth G] MOL2 format, chain ZA [auth G] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain EB [auth H] mmCIF format, chain FB [auth H] mmCIF format, chain KA [auth E] mmCIF format, chain LA [auth E] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain RA [auth F] mmCIF format, chain SA [auth F] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain YA [auth G] mmCIF format, chain ZA [auth G]	DA [auth D] EA [auth D] EB [auth H] FB [auth H] KA [auth E] DA [auth D], EA [auth D], EB [auth H], FB [auth H], KA [auth E], LA [auth E], N [auth A], O [auth A], RA [auth F], SA [auth F], T [auth B], U [auth B], X [auth C], Y [auth C], YA [auth G], ZA [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain EB [auth H] Focus chain FB [auth H] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain N [auth A] Focus chain O [auth A] Focus chain RA [auth F] Focus chain SA [auth F] Focus chain T [auth B] Focus chain U [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain YA [auth G] Focus chain ZA [auth G] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain EB [auth H] Focus chain FB [auth H] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain N [auth A] Focus chain O [auth A] Focus chain RA [auth F] Focus chain SA [auth F] Focus chain T [auth B] Focus chain U [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain YA [auth G] Focus chain ZA [auth G]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain AB [auth G] SDF format, chain BB [auth G] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain GB [auth H] SDF format, chain HA [auth D] SDF format, chain MA [auth E] SDF format, chain NA [auth E] SDF format, chain P [auth A] SDF format, chain R [auth A] SDF format, chain TA [auth F] SDF format, chain V [auth B] SDF format, chain VA [auth F] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain AB [auth G] MOL2 format, chain BB [auth G] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain GB [auth H] MOL2 format, chain HA [auth D] MOL2 format, chain MA [auth E] MOL2 format, chain NA [auth E] MOL2 format, chain P [auth A] MOL2 format, chain R [auth A] MOL2 format, chain TA [auth F] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth F] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain AB [auth G] mmCIF format, chain BB [auth G] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain GB [auth H] mmCIF format, chain HA [auth D] mmCIF format, chain MA [auth E] mmCIF format, chain NA [auth E] mmCIF format, chain P [auth A] mmCIF format, chain R [auth A] mmCIF format, chain TA [auth F] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth F] mmCIF format, chain Z [auth C]	AA [auth C] AB [auth G] BB [auth G] FA [auth D] GA [auth D] AA [auth C], AB [auth G], BB [auth G], FA [auth D], GA [auth D], GB [auth H], HA [auth D], MA [auth E], NA [auth E], P [auth A], R [auth A], TA [auth F], V [auth B], VA [auth F], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain AB [auth G] Focus chain BB [auth G] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain GB [auth H] Focus chain HA [auth D] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain P [auth A] Focus chain R [auth A] Focus chain TA [auth F] Focus chain V [auth B] Focus chain VA [auth F] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth G] Focus chain BB [auth G] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain GB [auth H] Focus chain HA [auth D] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain P [auth A] Focus chain R [auth A] Focus chain TA [auth F] Focus chain V [auth B] Focus chain VA [auth F] Focus chain Z [auth C]
POL Query on POL Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CB [auth G] SDF format, chain OA [auth E] SDF format, chain Q [auth A] SDF format, chain UA [auth F] MOL2 format, chain BA [auth C] MOL2 format, chain CB [auth G] MOL2 format, chain OA [auth E] MOL2 format, chain Q [auth A] MOL2 format, chain UA [auth F] mmCIF format, chain BA [auth C] mmCIF format, chain CB [auth G] mmCIF format, chain OA [auth E] mmCIF format, chain Q [auth A] mmCIF format, chain UA [auth F]	BA [auth C], CB [auth G], OA [auth E], Q [auth A], UA [auth F]	N-PROPANOL C₃ H₈ O BDERNNFJNOPAEC-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CB [auth G] Focus chain OA [auth E] Focus chain Q [auth A] Focus chain UA [auth F] Interactions & Density Focus chain BA [auth C] Focus chain CB [auth G] Focus chain OA [auth E] Focus chain Q [auth A] Focus chain UA [auth F]
K Query on K Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain M [auth A] SDF format, chain QA [auth F] SDF format, chain S [auth B] SDF format, chain W [auth C] SDF format, chain XA [auth G] SDF format, chain DB [auth H] SDF format, chain JA [auth E] MOL2 format, chain CA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain QA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain W [auth C] MOL2 format, chain XA [auth G] MOL2 format, chain DB [auth H] MOL2 format, chain JA [auth E] mmCIF format, chain CA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain QA [auth F] mmCIF format, chain S [auth B] mmCIF format, chain W [auth C] mmCIF format, chain XA [auth G] mmCIF format, chain DB [auth H] mmCIF format, chain JA [auth E]	CA [auth D] DB [auth H] JA [auth E] M [auth A] QA [auth F] CA [auth D], DB [auth H], JA [auth E], M [auth A], QA [auth F], S [auth B], W [auth C], XA [auth G]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain DB [auth H] Focus chain JA [auth E] Focus chain M [auth A] Focus chain QA [auth F] Focus chain S [auth B] Focus chain W [auth C] Focus chain XA [auth G] Interactions & Density Focus chain CA [auth D] Focus chain DB [auth H] Focus chain JA [auth E] Focus chain M [auth A] Focus chain QA [auth F] Focus chain S [auth B] Focus chain W [auth C] Focus chain XA [auth G]