6WIF | pdb_00006wif

Class C beta-lactamase from Acinetobacter baumannii in complex with 4-(Ethyl(methyl)carbamoyl)phenyl boronic acid

PDB DOI: https://doi.org/10.2210/pdb6WIF/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Acinetobacter baumannii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-04-09 Released: 2020-04-22
Deposition Author(s): Chang, C., Maltseva, N., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.240 (Depositor), 0.239 (DCC)
R-Value Work:
0.193 (Depositor), 0.193 (DCC)
R-Value Observed:
0.195 (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

class C beta-lactamase from Acinetobacter baumannii in complex with 4-(Ethyl(methyl)carbamoyl)phenyl boronic acid

Chang, C., Maltseva, N., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 164.66 kDa
Atom Count: 12,213
Modeled Residue Count: 1,428
Deposited Residue Count: 1,440
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B, C, D	360	Acinetobacter baumannii	Mutation(s): 0 Gene Names: ampC, A7M79_07980, A7M90_05015, BGC29_02775, E5294_06010, FJU36_01670, LV38_01949 EC: 3.5.2.6
UniProt
Find proteins for D6NSN2 (Acinetobacter baumannii) Explore D6NSN2 Go to UniProtKB: D6NSN2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D6NSN2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain W [auth D] SDF format, chain O [auth C] SDF format, chain N [auth C] MOL2 format, chain J [auth B] MOL2 format, chain W [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] mmCIF format, chain J [auth B] mmCIF format, chain W [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C]	J [auth B], N [auth C], O [auth C], W [auth D]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain W [auth D] Interactions & Density Focus chain J [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain W [auth D]
U2Y (Subject of Investigation/LOI) Query on U2Y Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain L [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain T [auth D] MOL2 format, chain L [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain T [auth D] mmCIF format, chain L [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], L [auth C], T [auth D]	{4-[ethyl(methyl)carbamoyl]phenyl}boronic acid C₁₀ H₁₄ B N O₃ AWXVNEUNYSIXAD-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain L [auth C] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain L [auth C] Focus chain T [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain P [auth C] SDF format, chain X [auth D] SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain Q [auth C] SDF format, chain M [auth C] SDF format, chain K [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain P [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain P [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B]	H [auth B] I [auth B] K [auth B] M [auth C] P [auth C] H [auth B], I [auth B], K [auth B], M [auth C], P [auth C], Q [auth C], U [auth D], V [auth D], X [auth D], Y [auth D], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain F [auth A] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain F [auth A] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain F [auth A]	F [auth A], R [auth C], S [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain R [auth C] Focus chain S [auth C] Interactions & Density Focus chain F [auth A] Focus chain R [auth C] Focus chain S [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.240 (Depositor), 0.239 (DCC)
R-Value Work: 0.193 (Depositor), 0.193 (DCC)
R-Value Observed: 0.195 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.244	α = 90
b = 80.925	β = 113.34
c = 104.377	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
SBC-Collect	data collection
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-04-22

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2020-04-22
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary