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.

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
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

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

Organizational Affiliation

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

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

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P52699
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OPS Query on OPS Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B]	3-OXO-3-[(3-OXOPROPYL)SULFANYL]PROPANE-1-THIOLATE C₆ H₉ O₂ S₂ LHLHVBHXBHTTIV-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain I [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain F [auth A]

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

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Entry History

Deposition Data

Released Date: 2005-06-21

Deposition Author(s):

Revision History (Full details and data files)

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