9QI6 | pdb_00009qi6

Structure of I105R BlaC from Mycobacterium tuberculosis bound to the trans-enamine adduct of clavulanic acid

PDB DOI: https://doi.org/10.2210/pdb9QI6/pdb

Classification: HYDROLASE
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-03-17 Released: 2025-06-11
Deposition Author(s): Chikunova, A., Radojkovic, M., Ubbink, M.
Funding Organization(s): Netherlands Organisation for Scientific Research (NWO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 ?
R-Value Free:
0.217 (Depositor), 0.203 (DCC)
R-Value Work:
0.186 (Depositor), 0.200 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

High-resolution activity and inhibitor profiling of residue 105 in class A beta-lactamases

Radojkovic, M., Koene, S.F., Chikunova, A., Timmer, M., Natarajan, S.V., Ubbink, M.

To be published.

Macromolecule Content

Total Structure Weight: 58.04 kDa
Atom Count: 4,461
Modeled Residue Count: 530
Deposited Residue Count: 530
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B	265	Mycobacterium tuberculosis	Mutation(s): 1 Gene Names: blaC, blaA, BQ2027_MB2094C EC: 3.5.2.6
UniProt
Find proteins for P0A5I7 (Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97)) Explore P0A5I7 Go to UniProtKB: P0A5I7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A5I7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ISS (Subject of Investigation/LOI) Query on ISS Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain S [auth B] MOL2 format, chain L [auth A] MOL2 format, chain S [auth B] mmCIF format, chain L [auth A] mmCIF format, chain S [auth B]	L [auth A], S [auth B]	(2E)-3-[(4-hydroxy-2-oxobutyl)amino]prop-2-enal C₇ H₁₁ N O₃ WWFGWBHKRFILGQ-HNQUOIGGSA-N		Interactions Focus chain L [auth A] Focus chain S [auth B] Interactions & Density Focus chain L [auth A] Focus chain S [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth B]	G [auth A], I [auth A], Q [auth B], R [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth A] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain G [auth A] Focus chain I [auth A] Focus chain Q [auth B] Focus chain R [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A], E [auth A], M [auth B], N [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain M [auth B] Focus chain N [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain F [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	F [auth A], J [auth A], K [auth A], O [auth B], P [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B]