6P87 Transferase Inhibitor date Jun 06, 2019
title E.Coli Lpxd In Complex With Compound 5
authors X.Ma, S.Shia
compound source
Molecule: Udp-3-O-(3-Hydroxymyristoyl)Glucosamine N-Acyltra
Chain: A, B, C
Synonym: Udp-3-O-(3-Ohc14)-Glcn N-Acyltransferase,Udp-3-O-( Hydroxytetradecanoyl)Glucosamine N-Acyltransferase;
Ec: 2.3.1.191
Engineered: Yes
 Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Lpxd, Lpxd_1, Lpxd_2, A8c65_17800, A9r57_04450, Ac789 Acn002_0184, Acn77_17005, Acn81_28485, Acu57_18525, Acu90_2 Am270_18210, Aml07_22885, Aml35_22825, Apz14_11060, Auq13_0 Aus26_23195, Aw059_09890, Aw106_08805, B1k96_12940, B7c53_0 Banra_00558, Banra_00653, Banra_02262, Banra_03350, Bet08_1 Bhf46_07835, Bhs81_00700, Bhs87_00855, Biz41_19025, Bjj90_2 Bk292_13720, Bk400_03560, Bmt53_09465, Bn17_46021, Btq06_06 Bue81_01655, Bvl39_02135, Bw690_02415, Bzl31_14885, C2u48_0 C4j69_03380, C5n07_08630, C5p01_08975, C5p43_07335, C6669_0 C6986_01145, C7235_20180, C7b06_05915, C7b07_04225, Ca593_0 Cg691_14440, Cg692_09445, Cg705_12975, Cg706_12690, Cod30_1 Cod46_06685, Cr538_20590, Cr539_04985, Crm83_15040, Cxb56_2 D0x26_09365, D2184_08545, D2185_20180, D2f89_01460, D3821_0 D3o91_03240, D3y67_16455, D9d20_18680, D9d55_03030, D9d69_0 D9e22_13300, D9e35_14480, D9g42_07535, D9h66_18155, D9h68_1 D9i18_15010, D9i87_01590, D9i97_03755, D9j11_16875, D9j44_1 Div22_06320, Dl545_20340, Dmz31_06810, Dnq41_04690, Dnq45_1 Dqf57_05615, Dqo13_06200, Ds732_05825, Dtl43_05870, Eai42_0 Eai46_03595, Eai52_11055, Ec1094v2_3672, Ec3234a_2c01610, Ec3426_00931, Ec382_03005, Ecto6_03883, Ed287_04550, Ed600_ Eep23_00115, Efv01_09910, Efv02_20465, Efv04_15215, Efv08_1 Efv11_08135, Efv12_18845, Efv15_17225, Efv17_09875, Eia13_1 El75_3585, El79_3695, El80_3642, Ers085374_03841, Ers150873 Ers150876_00054, Forc28_5013, Hw43_04650, Jd73_13090, Nctc10429_04183, Nctc10865_05054, Nctc11022_04906, Nctc1112 Nctc13462_02218, Nctc8500_04533, Nctc8960_01551, Nctc9037_0 Nctc9045_04699, Nctc9055_00956, Nctc9058_02808, Nctc9062_04 Nctc9706_01326, Nctc9969_04255, Pu06_22990, Rg28_03860, Rk5 Rx35_04913, Samea3472043_02537, Samea3472044_04146, Samea3472047_02509, Samea3472070_02384, Samea3472080_03763, Samea3472114_03609, Samea3484427_01386, Samea3484429_01095, Samea3752553_02884, Samea3752557_00885, Samea3752559_03701, Samea3753064_03381, Samea3753097_03916, Samea3753290_00404, Samea3753300_01852, Sk85_00179, Wq89_09605, Wr15_02380;
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet24a
symmetry Space Group: P 32 2 1
R_factor 0.180 R_Free 0.207
crystal
cell
length a length b length c angle alpha angle beta angle gamma
97.213 97.213 216.185 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.90 Å
ligand MG, O3V, O4P enzyme Transferase E.C.2.3.1.191 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceStructural and Biological Basis of Small Molecule Inhibition of Escherichia coli LpxD Acyltransferase Essential for Lipopolysaccharide Biosynthesis., Ma X, Prathapam R, Wartchow C, Chie-Leon B, Ho CM, De Vicente J, Han W, Li M, Lu Y, Ramurthy S, Shia S, Steffek M, Uehara T, ACS Infect Dis. 2019 Aug 22. doi: 10.1021/acsinfecdis.9b00127. PMID:31402665
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (353 Kb) [Save to disk]
  • Biological Unit Coordinates (6p87.pdb1.gz) 345 Kb
  • LPC: Ligand-Protein Contacts for 6P87
  • CSU: Contacts of Structural Units for 6P87
  • Structure Factors (3983 Kb)
  • Retrieve 6P87 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6P87 from S2C, [Save to disk]
    • View 6P87 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 6P87
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6p87_C] [6p87_A] [6p87_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6P87
  • Community annotation for 6P87 at PDBWiki (http://pdbwiki.org)

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