1VGN | pdb_00001vgn

Structure-based design of the irreversible inhibitors to metallo--lactamase (IMP-1)

• PDB DOI: https://doi.org/10.2210/pdb1VGN/pdb

• Classification: HYDROLASE
• Organism(s): Serratia marcescens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-04-27 Released: 2005-06-21 
• Deposition Author(s): Kurosaki, H., Yamaguchi, Y., Higashi, T., Soga, K., Matsueda, S., Misumi, S., Yamagata, Y., Arakawa, Y., Goto, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free: 
  0.243 (Depositor) 
• R-Value Work: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Irreversible Inhibition of Metallo-beta-lactamase (IMP-1) by 3-(3-Mercaptopropionylsulfanyl)propionic Acid Pentafluorophenyl Ester

Kurosaki, H., Yamaguchi, Y., Higashi, T., Soga, K., Matsueda, S., Yumoto, H., Misumi, S., Yamagata, Y., Arakawa, Y., Goto, M.

(2005) Angew Chem Int Ed Engl 44: 3861-3864

• PubMed: 15892033 
• DOI: https://doi.org/10.1002/anie.200500835
• Primary Citation Related Structures: 
  1VGN

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Organizational Affiliation: 
• Department of Structure-Function Physical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, Oe-honmachi 5-1, Kumamoto 862-0973, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 50.97 kDa 
• Atom Count: 3,513 
• Modeled Residue Count: 435 
• Deposited Residue Count: 456 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase IMP-1	A, B	228	Serratia marcescens	Mutation(s): 0  EC: 3.5.2.6 (PDB Primary Data), 3.1.26 (UniProt)
UniProt
Find proteins for P52699 (Serratia marcescens) Explore P52699  Go to UniProtKB:  P52699

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OPS	E [auth A], I [auth B]	3-OXO-3-[(3-OXOPROPYL)SULFANYL]PROPANE-1-THIOLATE C6 H9 O2 S2 LHLHVBHXBHTTIV-UHFFFAOYSA-M
ZN	C [auth A], D [auth A], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACY	F [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free:  0.243 (Depositor) 
• R-Value Work:  0.228 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.987	α = 90
b = 53.314	β = 90
c = 196.344	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-21 
Deposition Author(s): Kurosaki, H., Yamaguchi, Y., Higashi, T., Soga, K., Matsueda, S., Misumi, S., Yamagata, Y., Arakawa, Y., Goto, M.

Revision History  

• Version 1.0: 2005-06-21
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary