7U9B | pdb_00007u9b

Crystal structure of indoline 7 with KPC-2

PDB DOI: https://doi.org/10.2210/pdb7U9B/pdb

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

Deposited: 2022-03-10 Released: 2023-03-15
Deposition Author(s): Akhtar, A., Chen, Y.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.227 (Depositor), 0.239 (DCC)
R-Value Work:
0.179 (Depositor)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Probing the binding hot spots of KPC-2 carbapenemase using reversible tetrazole-based inhibitors

DeFrees, K., Cambeis, E.M., Chen, Y., Renslo, A.R.

To be published.

Macromolecule Content

Total Structure Weight: 28.81 kDa
Atom Count: 2,140
Modeled Residue Count: 268
Deposited Residue Count: 268
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbapenem-hydrolyzing beta-lactamase KPC	A	268	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
M2I (Subject of Investigation/LOI) Query on M2I Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	[(3S)-3-(1H-tetrazol-5-yl)-2,3-dihydro-1H-indol-1-yl][3-(trifluoromethyl)phenyl]methanone C₁₇ H₁₂ F₃ N₅ O ANOXZICGUBIZRA-CYBMUJFWSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.227 (Depositor), 0.239 (DCC)
R-Value Work: 0.179 (Depositor)
R-Value Observed: 0.181 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.71	α = 90
b = 58.91	β = 90
c = 76.66	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-03-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI161762

Revision History (Full details and data files)

Version 1.0: 2023-03-15
Type: Initial release
Version 1.1: 2023-10-25
Changes: Data collection, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.