8I52 | pdb_00008i52

Crystal structure of VIM-2 metallo-beta-lactamase in complex with 10-HHIA

PDB DOI: https://doi.org/10.2210/pdb8I52/pdb

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

Deposited: 2023-01-23 Released: 2024-01-10
Deposition Author(s): Wachino, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free:
0.178 (Depositor), 0.192 (DCC)
R-Value Work:
0.147 (Depositor), 0.160 (DCC)

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

Crystal structure of VIM-2 Metallo-beta-lactamase in complex with 10-HHIA

Wachino, J.

To be published.

Macromolecule Content

Total Structure Weight: 53.05 kDa
Atom Count: 4,250
Modeled Residue Count: 462
Deposited Residue Count: 492
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase class B VIM-2	A, B [auth D]	246	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, blm, VIM-2, PAERUG_P32_London_17_VIM_2_10_11_06255 EC: 3.5.2.6
UniProt
Find proteins for Q9K2N0 (Pseudomonas aeruginosa) Explore Q9K2N0 Go to UniProtKB: Q9K2N0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9K2N0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OR6 (Subject of Investigation/LOI) Query on OR6 Download:Ideal Coordinates CCD File SDF format, chain M [auth D] MOL2 format, chain M [auth D] mmCIF format, chain M [auth D]	M [auth D]	(2~{S})-2-butyl-3-methylidene-butanedioic acid C₉ H₁₄ O₄ ULDVOPUXMRCBDH-ZETCQYMHSA-N		Interactions Focus chain M [auth D] Interactions & Density Focus chain M [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain J [auth D] SDF format, chain I [auth D] SDF format, chain H [auth D] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain J [auth D] MOL2 format, chain I [auth D] MOL2 format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain J [auth D] mmCIF format, chain I [auth D] mmCIF format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] H [auth D] I [auth D] C [auth A], D [auth A], E [auth A], H [auth D], I [auth D], J [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth D] Focus chain I [auth D] Focus chain J [auth D] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth D] Focus chain I [auth D] Focus chain J [auth D]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain K [auth D] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain K [auth D] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain K [auth D] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], K [auth D], L [auth D]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth D] Focus chain L [auth D]