7M1Z

Targeting Enterococcus faecalis HMG-CoA reductase with a novel non-statin inhibitor

PDB DOI: https://doi.org/10.2210/pdb7M1Z/pdb

Classification: ANTIBIOTIC
Organism(s): Enterococcus faecalis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-03-15 Released: 2022-09-21
Deposition Author(s): Bose, S., Steussy, C.N., Stauffacher, C.V.
Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/National Center for Research Resources (NIH/NCRR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.239
R-Value Work: 0.196
R-Value Observed: 0.198

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

Targeting Enterococcus faecalis HMG-CoA reductase with a non-statin inhibitor

Bose, S., Steussy, C.N., Lopez-Perez, D., Schmidt, T., Kulathunga, S.C., Seleem, M.N., Lipton, M., Mesecar, A.D., Rodwell, V.W., Stauffacher, C.V.

(2023) Nat Commun

DOI: https://doi.org/10.1038/s42003-023-04639-y

Macromolecule Content

Total Structure Weight: 192.9 kDa
Atom Count: 12,803
Modelled Residue Count: 1,562
Deposited Residue Count: 1,720
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxymethylglutaryl-CoA reductase, degradative	A, B, C, D	430	Enterococcus faecalis	Mutation(s): 0 Gene Names: G5T22_00100 EC: 1.1.1.88 (PDB Primary Data), 2.3.1.9 (UniProt)
UniProt
Find proteins for Q835L3 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q835L3 Go to UniProtKB: Q835L3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q835L3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HMG Query on HMG Download Ideal Coordinates CCD File SDF format, chain Q [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain Q [auth B]	Q [auth B]	3-HYDROXY-3-METHYLGLUTARYL-COENZYME A C₂₇ H₃₉ N₇ O₂₀ P₃ S CABVTRNMFUVUDM-VRHQGPGLSA-I		Interactions Focus chain Q [auth B] Interactions & Density Focus chain Q [auth B]
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain EA [auth D] SDF format, chain R [auth B] SDF format, chain X [auth C] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain X [auth C] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain X [auth C]	E [auth A], EA [auth D], R [auth B], X [auth C]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain EA [auth D] Focus chain R [auth B] Focus chain X [auth C] Interactions & Density Focus chain E [auth A] Focus chain EA [auth D] Focus chain R [auth B] Focus chain X [auth C]
MEV Query on MEV Download Ideal Coordinates CCD File SDF format, chain W [auth C] MOL2 format, chain W [auth C] mmCIF format, chain W [auth C]	W [auth C]	(R)-MEVALONATE C₆ H₁₁ O₄ KJTLQQUUPVSXIM-ZCFIWIBFSA-M		Interactions Focus chain W [auth C] Interactions & Density Focus chain W [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	F [auth A] G [auth A] H [auth A] S [auth B] T [auth B] F [auth A], G [auth A], H [auth A], S [auth B], T [auth B], Y [auth C], Z [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain V [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain V [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain V [auth B]	CA [auth C] DA [auth C] K [auth A] L [auth A] M [auth A] CA [auth C], DA [auth C], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], V [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain V [auth B] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain V [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain U [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain U [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain U [auth B]	AA [auth C] BA [auth C] FA [auth D] GA [auth D] I [auth A] AA [auth C], BA [auth C], FA [auth D], GA [auth D], I [auth A], J [auth A], U [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain U [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain U [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.239
R-Value Work: 0.196
R-Value Observed: 0.198
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 241.289	α = 90
b = 62.557	β = 133.49
c = 171.925	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-09-21

Deposition Author(s):

Bose, S.

Steussy, C.N.

Stauffacher, C.V.

Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL52115
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	MH082373