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- PDB-3uhm: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase in c... -

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Basic information

Entry
Database: PDB / ID: 3uhm
TitleUDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase in complex with inhibitor
ComponentsUDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
KeywordsHydrolase/Hydrolase inhibitor / Amidohydrolases / Anti-Bacterial Agents / Bacteria / Catalytic Domain / Drug Design / Enzyme Inhibitors / Gram Negative / Hydrolase-Hydrolase inhibitor complex
Function / homology
Function and homology information


UDP-3-O-acyl-N-acetylglucosamine deacetylase / UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity / UDP-3-O-acyl-N-acetylglucosamine deacetylase activity / lipid A biosynthetic process / metal ion binding
Similarity search - Function
lpxc deacetylase, domain 1 / lpxc deacetylase, domain 2 / lpxc deacetylase, domain 1 / UDP-3-O-acyl N-acetylglucosamine deacetylase / UDP-3-O-acyl N-acetylglucosamine deacetylase, C-terminal / UDP-3-O-acyl N-acetylglucosamine deacetylase, N-terminal / UDP-3-O-acyl N-acetylglycosamine deacetylase / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANIDINE / Chem-RFN / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsMontgomery, J. / Liu, S.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Pyridone methylsulfone hydroxamate LpxC inhibitors for the treatment of serious gram-negative infections.
Authors: Montgomery, J.I. / Brown, M.F. / Reilly, U. / Price, L.M. / Abramite, J.A. / Arcari, J. / Barham, R. / Che, Y. / Chen, J.M. / Chung, S.W. / Collantes, E.M. / Desbonnet, C. / Doroski, M. / ...Authors: Montgomery, J.I. / Brown, M.F. / Reilly, U. / Price, L.M. / Abramite, J.A. / Arcari, J. / Barham, R. / Che, Y. / Chen, J.M. / Chung, S.W. / Collantes, E.M. / Desbonnet, C. / Doroski, M. / Doty, J. / Engtrakul, J.J. / Harris, T.M. / Huband, M. / Knafels, J.D. / Leach, K.L. / Liu, S. / Marfat, A. / McAllister, L. / McElroy, E. / Menard, C.A. / Mitton-Fry, M. / Mullins, L. / Noe, M.C. / O'Donnell, J. / Oliver, R. / Penzien, J. / Plummer, M. / Shanmugasundaram, V. / Thoma, C. / Tomaras, A.P. / Uccello, D.P. / Vaz, A. / Wishka, D.G.
History
DepositionNov 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6985
Polymers33,1471
Non-polymers5514
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.138, 80.965, 49.779
Angle α, β, γ (deg.)90.00, 95.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase / Protein envA / UDP-3-O-acyl-GlcNAc deacetylase


Mass: 33146.617 Da / Num. of mol.: 1 / Mutation: C40S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: lpxC, envA, PA4406 / Plasmid: PET21B / Production host: Escherichia coli (E. coli)
References: UniProt: P47205, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 5 types, 246 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-RFN / (2R)-N-hydroxy-2-methyl-2-(methylsulfonyl)-4-(2-oxo-4-phenylpyridin-1(2H)-yl)butanamide


Mass: 364.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N2O5S
#4: Chemical ChemComp-GAI / GUANIDINE / Guanidine


Mass: 59.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH5N3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.46 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.26→50 Å / Num. obs: 48477 / % possible obs: 66.7 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 9.37 Å2 / Rmerge(I) obs: 0.046
Reflection shellResolution: 1.26→1.31 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.087 / Mean I/σ(I) obs: 7.4 / % possible all: 73

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Processing

SoftwareName: BUSTER / Version: 2.11.2 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2VES

2ves


Resolution: 1.26→12.7 Å / Cor.coef. Fo:Fc: 0.9224 / Cor.coef. Fo:Fc free: 0.9138 / SU R Cruickshank DPI: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2008 2441 5.04 %RANDOM
Rwork0.1798 ---
obs0.1809 48435 66.87 %-
Displacement parametersBiso mean: 15.21 Å2
Baniso -1Baniso -2Baniso -3
1--1.1756 Å20 Å2-0.8194 Å2
2---0.8608 Å20 Å2
3---2.0364 Å2
Refine analyzeLuzzati coordinate error obs: 0.166 Å
Refinement stepCycle: LAST / Resolution: 1.26→12.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2334 0 34 242 2610
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012418HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.13268HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d859SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes63HARMONIC2
X-RAY DIFFRACTIONt_gen_planes360HARMONIC5
X-RAY DIFFRACTIONt_it2418HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.61
X-RAY DIFFRACTIONt_other_torsion13.28
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion312SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3095SEMIHARMONIC4
LS refinement shellResolution: 1.26→1.29 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3391 12 4.23 %
Rwork0.1932 272 -
all0.1988 284 -
obs--66.87 %
Refinement TLS params.Method: refined / Origin x: 1.3124 Å / Origin y: 0.0605 Å / Origin z: 6.9198 Å
111213212223313233
T0.0051 Å20.0051 Å2-0.0004 Å2-0.0087 Å2-0.0036 Å2--0.0044 Å2
L0.2472 °20.0131 °2-0.0189 °2-0.3767 °20.0467 °2--0.2108 °2
S0.0068 Å °-0.0156 Å °-0.0033 Å °-0.0083 Å °0.0016 Å °-0.0077 Å °0.0131 Å °0.0113 Å °-0.0084 Å °
Refinement TLS groupSelection details: { A|1 - A|303 }

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