9F0Q | pdb_00009f0q

VIM-2 in complex with GKV53 (5d) - dynamically chiral phosphonic acid-type metallo-beta-lactamase inhibitors

PDB DOI: https://doi.org/10.2210/pdb9F0Q/pdb

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

Deposited: 2024-04-17 Released: 2025-04-30
Deposition Author(s): Bartels, K., Prester, A., Bosman, R., Gulyas, K.V., Erdelyi, M., Schulz, E.C.
Funding Organization(s): German Federal Ministry for Education and Research, German Research Foundation (DFG), Max Planck Society, Swedish Research Council, Uppsala Antibiotic Center

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.213 (Depositor), 0.214 (DCC)
R-Value Work:
0.171 (Depositor), 0.171 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Dynamically chiral phosphonic acid-type metallo-beta-lactamase inhibitors

Gulyas, K.V., Salamonsen, D., Zhou, L., Tamasi, V., Rasmussen, A.A., Thoma, J., Prester, A., Bartels, K.B., Bosman, R., Haffke, P., Rohde, H., Csala, M., Leiros, H.K.S., Schulz, E.C., Zhu, W., Erdelyi, M.

To be published.

Macromolecule Content

Total Structure Weight: 56.37 kDa
Atom Count: 4,099
Modelled Residue Count: 462
Deposited Residue Count: 508
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metallo-beta-lactamase type 2	A, B	254	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: blaVIM EC: 3.5.2.6
UniProt
Find proteins for B8QIQ9 (Pseudomonas aeruginosa) Explore B8QIQ9 Go to UniProtKB: B8QIQ9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B8QIQ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IJ9 (Subject of Investigation/LOI) Query on A1IJ9 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B]	E [auth A], L [auth B]	[(S)-(1-benzothiophen-3-ylcarbonylamino)-(2-hydroxyphenyl)methyl]phosphonic acid C₁₆ H₁₄ N O₅ P S AIGFEXSDJRIIRW-INIZCTEOSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B]
A1H8W Query on A1H8W Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	[(R)-(1-benzothiophen-3-ylcarbonylamino)-(2-hydroxyphenyl)methyl]phosphonic acid C₁₆ H₁₄ N O₅ P S AIGFEXSDJRIIRW-MRXNPFEDSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	F [auth A] G [auth A] H [auth A] M [auth B] N [auth B] F [auth A], G [auth A], H [auth A], M [auth B], N [auth B], O [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	C [auth A], D [auth A], I [auth B], J [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain I [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.213 (Depositor), 0.214 (DCC)
R-Value Work: 0.171 (Depositor), 0.171 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.804	α = 90
b = 79.021	β = 130.76
c = 67.815	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
autoPROC	data processing
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-30

Deposition Author(s):

Funding Organization	Location	Grant Number
German Federal Ministry for Education and Research	Germany	01KI2114
German Research Foundation (DFG)	Germany	458246365
Max Planck Society	Germany	--
Swedish Research Council	Sweden	2013-8804
Uppsala Antibiotic Center	Sweden	--