6BOI

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
R-Value Work: 0.162
R-Value Observed: 0.164

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 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
Modelled Residue Count: 704
Deposited Residue Count: 704
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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]	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 D [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain D [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B]	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 L [auth A] SDF format, chain M [auth A] SDF format, chain S [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain S [auth B]	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 Q [auth B] SDF format, chain R [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 Q [auth B] MOL2 format, chain R [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]