6BOI | pdb_00006boi

Crystal Structure of LdtMt2 (56-408) with a panipenem adduct at the active site cysteine-354

PDB DOI: https://doi.org/10.2210/pdb6BOI/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis H37Ra
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-11-20 Released: 2018-04-11
Deposition Author(s): Saavedra, H., Bianchet, M.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.201 (Depositor), 0.206 (DCC)
R-Value Work:
0.162 (Depositor)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structures and Mechanism of Inhibition of Mycobacterium tuberculosis L,D-transpeptidase 2 by Panipenem

Saavedra, H., Bianchet, M.A.

To be published.

Macromolecule Content

Total Structure Weight: 77.58 kDa
Atom Count: 5,963
Modeled Residue Count: 704
Deposited Residue Count: 704
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative conserved lipoprotein LppS	A, B	352	Mycobacterium tuberculosis H37Ra	Mutation(s): 0 Gene Names: lppS, MRA_2545
UniProt
Find proteins for A5U5L6 (Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra)) Explore A5U5L6 Go to UniProtKB: A5U5L6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5U5L6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
E0Y Query on E0Y Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain N [auth B] MOL2 format, chain C [auth A] MOL2 format, chain N [auth B] mmCIF format, chain C [auth A] mmCIF format, chain N [auth B]	C [auth A], N [auth B]	(3S,5R)-5-[(2R,3R)-1,3-dihydroxybutan-2-yl]-3-({(3R)-1-[(1E)-ethanimidoyl]pyrrolidin-3-yl}sulfanyl)-L-proline C₁₅ H₂₇ N₃ O₄ S BSDSVSWWQWOWPI-SXFXLBHASA-N		Interactions Focus chain C [auth A] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain N [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain D [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain D [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain D [auth A]	D [auth A], O [auth B], P [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain D [auth A] Focus chain O [auth B] Focus chain P [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain S [auth B] SDF format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain S [auth B] MOL2 format, chain L [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain S [auth B] mmCIF format, chain L [auth A]	J [auth A], K [auth A], L [auth A], M [auth A], S [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain S [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain S [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File 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 I [auth A] SDF format, chain R [auth B] SDF format, chain Q [auth B] 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 I [auth A] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], Q [auth B], R [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth B] Focus chain R [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.201 (Depositor), 0.206 (DCC)
R-Value Work: 0.162 (Depositor)
R-Value Observed: 0.164 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.06	α = 90
b = 94.06	β = 92.7
c = 75.4	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-04-11

Deposition Author(s):

Saavedra, H.

Bianchet, M.A.

Revision History (Full details and data files)

Version 1.0: 2018-04-11
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary