7O5Q | pdb_00007o5q

Crystal Structure of a Class D Carbapenemase Complexed with Hydrolyzed Oxacillin

PDB DOI: https://doi.org/10.2210/pdb7O5Q/pdb

Classification: HYDROLASE
Organism(s): Klebsiella pneumoniae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-04-09 Released: 2022-04-20
Deposition Author(s): Zhou, Q., He, Y., Jin, Y.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.211 (Depositor), 0.220 (DCC)
R-Value Work:
0.173 (Depositor), 0.180 (DCC)

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

Crystal Structure of a Class D Carbapenemase Complexed with Hydrolyzed Oxacillin

Zhou, Q., He, Y., Jin, Y.

To be published.

Macromolecule Content

Total Structure Weight: 125.14 kDa
Atom Count: 8,888
Modelled Residue Count: 968
Deposited Residue Count: 1,040
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 [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	260	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: bla OXA-48, bla_2, blaOXA-48, G5637_27540, KPE71T_00045, SAMEA3649466_05396 EC: 3.5.2.6
UniProt
Find proteins for Q6XEC0 (Klebsiella pneumoniae) Explore Q6XEC0 Go to UniProtKB: Q6XEC0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6XEC0
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
V3H (Subject of Investigation/LOI) Query on V3H Download Ideal Coordinates CCD File SDF format, chain S [auth CCC] SDF format, chain Z [auth DDD] MOL2 format, chain S [auth CCC] MOL2 format, chain Z [auth DDD] mmCIF format, chain S [auth CCC] mmCIF format, chain Z [auth DDD]	S [auth CCC], Z [auth DDD]	(2R,4S)-2-[(1R)-2-butoxy-1-[(5-methyl-3-phenyl-1,2-oxazol-4-yl)carbonylamino]-2-oxidanylidene-ethyl]-5,5-dimethyl-1,3-thiazolidin-3-ium-4-carboxylic acid C₂₃ H₃₀ N₃ O₆ S KTVAJMKGNMTGBA-CMKODMSKSA-O		Interactions Focus chain S [auth CCC] Focus chain Z [auth DDD] Interactions & Density Focus chain S [auth CCC] Focus chain Z [auth DDD]
0WO (Subject of Investigation/LOI) Query on 0WO Download Ideal Coordinates CCD File SDF format, chain Q [auth CCC] SDF format, chain X [auth DDD] MOL2 format, chain Q [auth CCC] MOL2 format, chain X [auth DDD] mmCIF format, chain Q [auth CCC] mmCIF format, chain X [auth DDD]	Q [auth CCC], X [auth DDD]	(2R,4S)-2-[(R)-carboxy{[(5-methyl-3-phenyl-1,2-oxazol-4-yl)carbonyl]amino}methyl]-5,5-dimethyl-1,3-thiazolidine-4-carbo xylic acid C₁₉ H₂₁ N₃ O₆ S JCHZLBSPYSDECZ-OFQRWUPVSA-N		Interactions Focus chain Q [auth CCC] Focus chain X [auth DDD] Interactions & Density Focus chain Q [auth CCC] Focus chain X [auth DDD]
IOD (Subject of Investigation/LOI) Query on IOD Download Ideal Coordinates CCD File SDF format, chain AA [auth DDD] SDF format, chain BA [auth DDD] SDF format, chain F [auth AAA] SDF format, chain G [auth AAA] SDF format, chain H [auth AAA] SDF format, chain I [auth AAA] SDF format, chain L [auth BBB] SDF format, chain M [auth BBB] SDF format, chain N [auth BBB] SDF format, chain O [auth BBB] SDF format, chain P [auth BBB] SDF format, chain T [auth CCC] SDF format, chain U [auth CCC] SDF format, chain V [auth CCC] SDF format, chain W [auth CCC] MOL2 format, chain AA [auth DDD] MOL2 format, chain BA [auth DDD] MOL2 format, chain F [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain L [auth BBB] MOL2 format, chain M [auth BBB] MOL2 format, chain N [auth BBB] MOL2 format, chain O [auth BBB] MOL2 format, chain P [auth BBB] MOL2 format, chain T [auth CCC] MOL2 format, chain U [auth CCC] MOL2 format, chain V [auth CCC] MOL2 format, chain W [auth CCC] mmCIF format, chain AA [auth DDD] mmCIF format, chain BA [auth DDD] mmCIF format, chain F [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain H [auth AAA] mmCIF format, chain I [auth AAA] mmCIF format, chain L [auth BBB] mmCIF format, chain M [auth BBB] mmCIF format, chain N [auth BBB] mmCIF format, chain O [auth BBB] mmCIF format, chain P [auth BBB] mmCIF format, chain T [auth CCC] mmCIF format, chain U [auth CCC] mmCIF format, chain V [auth CCC] mmCIF format, chain W [auth CCC]	AA [auth DDD] BA [auth DDD] F [auth AAA] G [auth AAA] H [auth AAA] AA [auth DDD], BA [auth DDD], F [auth AAA], G [auth AAA], H [auth AAA], I [auth AAA], L [auth BBB], M [auth BBB], N [auth BBB], O [auth BBB], P [auth BBB], T [auth CCC], U [auth CCC], V [auth CCC], W [auth CCC]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain AA [auth DDD] Focus chain BA [auth DDD] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain L [auth BBB] Focus chain M [auth BBB] Focus chain N [auth BBB] Focus chain O [auth BBB] Focus chain P [auth BBB] Focus chain T [auth CCC] Focus chain U [auth CCC] Focus chain V [auth CCC] Focus chain W [auth CCC] Interactions & Density Focus chain AA [auth DDD] Focus chain BA [auth DDD] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain L [auth BBB] Focus chain M [auth BBB] Focus chain N [auth BBB] Focus chain O [auth BBB] Focus chain P [auth BBB] Focus chain T [auth CCC] Focus chain U [auth CCC] Focus chain V [auth CCC] Focus chain W [auth CCC]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth AAA] SDF format, chain J [auth BBB] SDF format, chain R [auth CCC] MOL2 format, chain E [auth AAA] MOL2 format, chain J [auth BBB] MOL2 format, chain R [auth CCC] mmCIF format, chain E [auth AAA] mmCIF format, chain J [auth BBB] mmCIF format, chain R [auth CCC]	E [auth AAA], J [auth BBB], R [auth CCC]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth AAA] Focus chain J [auth BBB] Focus chain R [auth CCC] Interactions & Density Focus chain E [auth AAA] Focus chain J [auth BBB] Focus chain R [auth CCC]
1BO Query on 1BO Download Ideal Coordinates CCD File SDF format, chain K [auth BBB] SDF format, chain Y [auth DDD] MOL2 format, chain K [auth BBB] MOL2 format, chain Y [auth DDD] mmCIF format, chain K [auth BBB] mmCIF format, chain Y [auth DDD]	K [auth BBB], Y [auth DDD]	1-BUTANOL C₄ H₁₀ O LRHPLDYGYMQRHN-UHFFFAOYSA-N		Interactions Focus chain K [auth BBB] Focus chain Y [auth DDD] Interactions & Density Focus chain K [auth BBB] Focus chain Y [auth DDD]