8HYB | pdb_00008hyb

Crystal structure of B1 IMP-1 MBL in complex with 2-amino-5-phenethylthiazole-4-carboxylic acid

PDB DOI: https://doi.org/10.2210/pdb8HYB/pdb

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

Deposited: 2023-01-06 Released: 2024-01-24
Deposition Author(s): Yan, Y.-H., Zhu, K.-R., Li, G.-B.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free:
0.227 (Depositor), 0.232 (DCC)
R-Value Work:
0.177 (Depositor), 0.188 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: in silico
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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

2-Aminothiazole-4-carboxylic acids as cross-class metallo-beta-lactamase inhibitors by mimicking beta-lactam hydrolysate binding

Yan, Y.-H., Zhu, K.-R., Yang, L.-L., Li, G.-B.

To be published.

Macromolecule Content

Total Structure Weight: 98.67 kDa
Atom Count: 7,099
Modeled Residue Count: 876
Deposited Residue Count: 876
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	219	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: blaIMP-1, bla IMP, bla-imp, blaESP, imp EC: 3.5.2.6
UniProt
Find proteins for Q79MP6 (Pseudomonas aeruginosa) Explore Q79MP6 Go to UniProtKB: Q79MP6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q79MP6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5ZX (Subject of Investigation/LOI) Query on 5ZX Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D]	G [auth A], M [auth B], P [auth C], T [auth D]	2-azanyl-5-(2-phenylethyl)-1,3-thiazole-4-carboxylic acid C₁₂ H₁₂ N₂ O₂ S JARXXMAFINZHLY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain G [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain T [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain U [auth D] MOL2 format, chain U [auth D] mmCIF format, chain U [auth D]	U [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain U [auth D] Interactions & Density Focus chain U [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain S [auth D] SDF format, chain R [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D]	E [auth A] F [auth A] K [auth B] L [auth B] N [auth C] E [auth A], F [auth A], K [auth B], L [auth B], N [auth C], O [auth C], R [auth D], S [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain Q [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain Q [auth C] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain Q [auth C]	H [auth A], I [auth A], J [auth A], Q [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain Q [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain Q [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.227 (Depositor), 0.232 (DCC)
R-Value Work: 0.177 (Depositor), 0.188 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.899	α = 90
b = 201.103	β = 89.97
c = 52.319	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
PHASER	phasing
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-01-24

Deposition Author(s):

Yan, Y.-H.

Zhu, K.-R.

Li, G.-B.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81874291
National Natural Science Foundation of China (NSFC)	China	82122065
National Natural Science Foundation of China (NSFC)	China	82073698