8IY4

Crystal structure of Class A beta-lactamase BlaA WT - complex with Meropenem

PDB DOI: https://doi.org/10.2210/pdb8IY4/pdb

Classification: ANTIMICROBIAL PROTEIN
Organism(s): Yersinia enterocolitica
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-04-03 Released: 2024-04-03
Deposition Author(s): Bhattacharya, S., Hazra, S.
Funding Organization(s): Indian Council of Medical Research, Science and Engineering Research Board (SERB)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.264
R-Value Work: 0.202

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of Class A beta-lactamase BlaA WT - complex with Meropenem

Bhattacharya, S., Hazra, S.

To be published.

Macromolecule Content

Total Structure Weight: 32.45 kDa
Atom Count: 2,203
Modelled Residue Count: 260
Deposited Residue Count: 294
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	294	Yersinia enterocolitica	Mutation(s): 0 Gene Names: blaA EC: 3.5.2.6
UniProt
Find proteins for Q01166 (Yersinia enterocolitica) Explore Q01166 Go to UniProtKB: Q01166
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q01166
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MER (Subject of Investigation/LOI) Query on MER Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	(4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid C₁₇ H₂₇ N₃ O₅ S DYQHXZPAIVAJRU-HTXLXMOSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PO4 (Subject of Investigation/LOI) Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.264
R-Value Work: 0.202
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.774	α = 90
b = 72.619	β = 94.953
c = 43.707	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrysalisPro	data collection
Coot	model building
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-04-03

Deposition Author(s):

Bhattacharya, S.

Hazra, S.

Funding Organization	Location	Grant Number
Indian Council of Medical Research	India	5/3/8/17/GIA-ITR
Indian Council of Medical Research	India	BIC/12(15)/2014,
Science and Engineering Research Board (SERB)	India	YSS/2014/000492

Revision History (Full details and data files)

Version 1.0: 2024-04-03
Type: Initial release

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8IY4

Crystal structure of Class A beta-lactamase BlaA WT - complex with Meropenem

Crystal structure of Class A beta-lactamase BlaA WT - complex with Meropenem

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)