7VQN | pdb_00007vqn

Crystal structure of KPC-2 beta-lactamase complexed with hydrolyzed EXW-1

PDB DOI: https://doi.org/10.2210/pdb7VQN/pdb

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

Deposited: 2021-10-20 Released: 2022-10-26
Deposition Author(s): Xie, H.X.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free:
0.206 (Depositor), 0.206 (DCC)
R-Value Work:
0.170 (Depositor), 0.170 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of KPC-2 beta-lactamase complexed with hydrolyzed EXW-1

Xie, H.X.

To be published.

Macromolecule Content

Total Structure Weight: 115.16 kDa
Atom Count: 8,702
Modeled Residue Count: 1,064
Deposited Residue Count: 1,064
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbapenem-hydrolyzing beta-lactamase KPC	A, B, C, D	266	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: bla, kpc, kpc1 EC: 3.5.2.6
UniProt
Find proteins for Q9F663 (Klebsiella pneumoniae) Explore Q9F663 Go to UniProtKB: Q9F663
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9F663
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7TC (Subject of Investigation/LOI) Query on 7TC Download:Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain Y [auth D] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain T [auth C] mmCIF format, chain Y [auth D]	T [auth C], Y [auth D]	(2R,3S)-3-methyl-4-methylidene-2-[(2S,3R)-3-oxidanyl-1-oxidanylidene-butan-2-yl]-2,3-dihydropyrrole-5-carboxylic acid C₁₁ H₁₅ N O₄ GGYAWCWTCNLFOB-KDBVAPGDSA-N		Interactions Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain T [auth C] Focus chain Y [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth B] E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth C], O [auth C], P [auth C], Q [auth C], R [auth C], S [auth C], U [auth D], V [auth D], W [auth D], X [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D]