8Y4I | pdb_00008y4i

Metal Beta-Lactamase VIM-2 in Complex with MBL inhibitor B7

PDB DOI: https://doi.org/10.2210/pdb8Y4I/pdb

Classification: METAL BINDING PROTEIN/INHIBITOR
Organism(s): Enterobacteriaceae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-01-30 Released: 2025-02-05
Deposition Author(s): Li, G.-B., Wang, S.-Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.244 (Depositor), 0.251 (DCC)
R-Value Work:
0.191 (Depositor), 0.201 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Discovery of 2-((1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-3-yl)methyl)acrylic acids as potent MBL inhibitors

Liang, G.-Q., Wang, S.-Y., Li, G.-B.

To be published.

Macromolecule Content

Total Structure Weight: 199.4 kDa
Atom Count: 14,264
Modeled Residue Count: 1,848
Deposited Residue Count: 1,848
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metal Beta-Lactamase VIM-2	A, B, C, D, E A, B, C, D, E, F, G, H	231	Enterobacteriaceae	Mutation(s): 0 Gene Names: blaVIM2 EC: 3.5.2.6
UniProt
Find proteins for A0A0F7KYQ8 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore A0A0F7KYQ8 Go to UniProtKB: A0A0F7KYQ8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0F7KYQ8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1LXF (Subject of Investigation/LOI) Query on A1LXF Download Ideal Coordinates CCD File SDF format, chain X [auth E] SDF format, chain U [auth D] SDF format, chain Q [auth C] SDF format, chain N [auth B] SDF format, chain K [auth A] SDF format, chain GA [auth H] SDF format, chain DA [auth G] SDF format, chain AA [auth F] MOL2 format, chain X [auth E] MOL2 format, chain U [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] MOL2 format, chain GA [auth H] MOL2 format, chain DA [auth G] MOL2 format, chain AA [auth F] mmCIF format, chain X [auth E] mmCIF format, chain U [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A] mmCIF format, chain GA [auth H] mmCIF format, chain DA [auth G] mmCIF format, chain AA [auth F]	AA [auth F] DA [auth G] GA [auth H] K [auth A] N [auth B] AA [auth F], DA [auth G], GA [auth H], K [auth A], N [auth B], Q [auth C], U [auth D], X [auth E]	2-[[(9R)-2-fluoranyl-7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1,3,5-trien-9-yl]methyl]prop-2-enoic acid C₁₁ H₁₁ B F O₅ CCVJYJDJQZZSRS-SECBINFHSA-N		Interactions Focus chain AA [auth F] Focus chain DA [auth G] Focus chain GA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain DA [auth G] Focus chain GA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain X [auth E]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain Y [auth F] SDF format, chain W [auth E] SDF format, chain V [auth E] SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain FA [auth H] SDF format, chain EA [auth H] SDF format, chain CA [auth G] SDF format, chain BA [auth G] MOL2 format, chain Z [auth F] MOL2 format, chain Y [auth F] MOL2 format, chain W [auth E] MOL2 format, chain V [auth E] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain FA [auth H] MOL2 format, chain EA [auth H] MOL2 format, chain CA [auth G] MOL2 format, chain BA [auth G] mmCIF format, chain Z [auth F] mmCIF format, chain Y [auth F] mmCIF format, chain W [auth E] mmCIF format, chain V [auth E] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain FA [auth H] mmCIF format, chain EA [auth H] mmCIF format, chain CA [auth G] mmCIF format, chain BA [auth G]	BA [auth G] CA [auth G] EA [auth H] FA [auth H] I [auth A] BA [auth G], CA [auth G], EA [auth H], FA [auth H], I [auth A], J [auth A], L [auth B], M [auth B], O [auth C], P [auth C], S [auth D], T [auth D], V [auth E], W [auth E], Y [auth F], Z [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth G] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain FA [auth H] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain V [auth E] Focus chain W [auth E] Focus chain Y [auth F] Focus chain Z [auth F] Interactions & Density Focus chain BA [auth G] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain FA [auth H] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain V [auth E] Focus chain W [auth E] Focus chain Y [auth F] Focus chain Z [auth F]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain R [auth C] MOL2 format, chain R [auth C] mmCIF format, chain R [auth C]	R [auth C]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain R [auth C] Interactions & Density Focus chain R [auth C]