5DCC

X-RAY CRYSTAL STRUCTURE OF a TEBIPENEM ADDUCT OF L,D TRANSPEPTIDASE 2 FROM MYCOBACTERIUM TUBERCULOSIS

PDB DOI: https://doi.org/10.2210/pdb5DCC/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis CDC1551
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-08-23 Released: 2016-09-28
Deposition Author(s): Pan, Y., Basta, L., Lamichhane, G., Bianchet, M.A.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.214
R-Value Work: 0.168
R-Value Observed: 0.173

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural insight into the inactivation of Mycobacterium tuberculosis non-classical transpeptidase LdtMt2 by biapenem and tebipenem.

Bianchet, M.A., Pan, Y.H., Basta, L.A.B., Saavedra, H., Lloyd, E.P., Kumar, P., Mattoo, R., Townsend, C.A., Lamichhane, G.

(2017) BMC Biochem 18: 8-8

PubMed: 28545389 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1186/s12858-017-0082-4
Primary Citation of Related Structures:
5D7H, 5DC2, 5DCC

PubMed Abstract:
The carbapenem subclass of β-lactams is among the most potent antibiotics available today. Emerging evidence shows that, unlike other subclasses of β-lactams, carbapenems bind to and inhibit non-classical transpeptidases (L,D-transpeptidases) that generate 3 → 3 linkages in bacterial peptidoglycan. The carbapenems biapenem and tebipenem exhibit therapeutically valuable potencies against Mycobacterium tuberculosis (Mtb).

Organizational Affiliation

Department of Neurology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA. bianchet@jhmi.edu.

Macromolecule Content

Total Structure Weight: 79.32 kDa
Atom Count: 6,020
Modelled Residue Count: 705
Deposited Residue Count: 706
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L,D-transpeptidase 2	A, B	353	Mycobacterium tuberculosis CDC1551	Mutation(s): 0 Gene Names: ldtB, MT2594, V735_02606 EC: 2.3.2
UniProt
Find proteins for I6Y9J2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6Y9J2 Go to UniProtKB: I6Y9J2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I6Y9J2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
58U Query on 58U Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain S [auth B] MOL2 format, chain C [auth A] MOL2 format, chain S [auth B]	C [auth A], S [auth B]	(4S)-4-methyl-2,5,7-trioxoheptanoic acid C₈ H₁₀ O₅ JDEHLHSRIXMJEO-YFKPBYRVSA-N		Interactions Focus chain C [auth A] Focus chain S [auth B] Interactions & Density Focus chain C [auth A] Focus chain S [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A]	DA [auth B] EA [auth B] FA [auth B] L [auth A] M [auth A] DA [auth B], EA [auth B], FA [auth B], L [auth A], M [auth A], N [auth A], O [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] I [auth A] J [auth A] AA [auth B], BA [auth B], CA [auth B], I [auth A], J [auth A], K [auth A], X [auth B], Y [auth B], Z [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], T [auth B], U [auth B], V [auth B], W [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A]	GA [auth B], HA [auth B], P [auth A], Q [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain GA [auth B] Focus chain HA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain GA [auth B] Focus chain HA [auth B] Focus chain P [auth A] Focus chain Q [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain IA [auth B] SDF format, chain R [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain R [auth A]	IA [auth B], R [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain IA [auth B] Focus chain R [auth A] Interactions & Density Focus chain IA [auth B] Focus chain R [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.214
R-Value Work: 0.168
R-Value Observed: 0.173
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.934	α = 90
b = 94.4	β = 92.88
c = 75.385	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-09-28

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R21AI111739

Revision History (Full details and data files)

Version 1.0: 2016-09-28
Type: Initial release
Version 1.1: 2017-08-23
Changes: Author supporting evidence, Database references, Derived calculations
Version 1.2: 2019-12-11
Changes: Author supporting evidence
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Refinement description