9ORB | pdb_00009orb

X-ray diffraction structure of the CTX-M-14 beta-lactamase-avibactam complex an inhibitor cocktail-soaked crystal

PDB DOI: https://doi.org/10.2210/pdb9ORB/pdb

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

Deposited: 2025-05-21 Released: 2025-06-18
Deposition Author(s): Vlahakis, N.W., Rodriguez, J.A., Jacobs, L.M.C., Chen, Y.
Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Science Foundation (NSF, United States), Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.175 (Depositor), 0.175 (DCC)
R-Value Work:
0.152 (Depositor), 0.152 (DCC)
R-Value Observed:
0.153 (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

Combining MicroED and native mass spectrometry for structural discovery of enzyme-small molecule complexes

Vlahakis, N.W., Flowers, C.W., Liu, M., Agdanowski, M., Johnson, S., Summers, J.A., Jacobs, L.M.C., Keyser, C., Russell, P., Rose, S., Orlans, J., Adhami, N., Chen, Y., Sawaya, M.R., Basu, S., De Sanctis, D., Chen, Y., Wakatsuki, S., Nelson, H.M., Loo, J.A., Tang, Y., Rodriguez, J.A.

To be published.

Macromolecule Content

Total Structure Weight: 56.63 kDa
Atom Count: 4,650
Modeled Residue Count: 524
Deposited Residue Count: 526
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B	263	Escherichia coli	Mutation(s): 0 Gene Names: blaCTX-M-14, beta-lactamase CTX-M-14, bla, bla CTX-M-14, bla-CTX-M-14a, blaCTX-M, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b... blaCTX-M-14, beta-lactamase CTX-M-14, bla, bla CTX-M-14, bla-CTX-M-14a, blaCTX-M, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, AM333_26030, AM340_28340, AM465_01285, AM465_06510, AM465_23360, APT94_14605, BEN53_26220, BJJ90_27545, BK334_27290, BOH76_00730, BON63_16015, BON65_15195, BON66_01305, BON69_22545, BON72_03470, BON75_10525, BON76_14325, BON83_15455, BON86_08515, BON91_02075, BON92_04750, BON94_23850, BON95_01680, BON96_03940, BON98_23175, BXT93_06855, C5N07_28500, CDL37_21060, CR538_26855, DW236_20870, E4K51_21070, EIA08_25160, EIA21_26975, ELT23_05930, ELV24_09995, ELX61_24095, EST51_15935, EST51_18575, EST51_22260, EST51_22365, ETN48_p0088, FNJ69_13810, FTV90_03295, GE096_24920, GE096_25355, GQE36_23945, HGR36_01450, HGR36_27140, HHH24_004455, HHH24_005319, HJI79_003882, HJI79_004995, HK427_004976, HK427_005087, HL152_24835, HL152_25835, HL563_21800, HL563_23665, HLT96_25270, HLT96_28700, HLU13_27785, HLY53_18605, HLY53_26190, HLZ85_26065, HMW26_20895, HMW26_29355, HNC73_28650, HNC75_27190, HNC75_29165, HNC80_26145, HNC80_27675, HNC88_26185, HNC88_27880, HND23_26750, HND23_28285, HNV91_23425, HNV91_24920, HNV94_24095, HNV94_27845, pCT_085, pHK01_011, RCS103_P0010, RCS30_P0082, RCS56_P0085, RCS60_P0031, RCS63_P0006, RCS65_P0008, RCS66_P0053, SAMEA4362930_00013, SAMEA4363083_00099, SAMEA4370290_00046, WP4S18E07_P40650, WP7S17E01_P10270, WP7S18E09_37980 EC: 3.5.2.6
UniProt
Find proteins for Q9L5C7 (Escherichia coli) Explore Q9L5C7 Go to UniProtKB: Q9L5C7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9L5C7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NXL (Subject of Investigation/LOI) Query on NXL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	(2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide C₇ H₁₃ N₃ O₆ S WJDGWXPPFHLLNL-RITPCOANSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.175 (Depositor), 0.175 (DCC)
R-Value Work: 0.152 (Depositor), 0.152 (DCC)
R-Value Observed: 0.153 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.21	α = 90
b = 107.19	β = 101.88
c = 47.92	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-06-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	HHMI-EPI
National Science Foundation (NSF, United States)	United States	DMR-1548924
Department of Energy (DOE, United States)	United States	DE-FC02-02ER63421