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- PDB-3mla: BaNadD in complex with inhibitor 1_02 -

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Basic information

Entry
Database: PDB / ID: 3mla
TitleBaNadD in complex with inhibitor 1_02
Componentsnicotinate-nucleotide adenylyltransferase
KeywordsTRANSFERASE / NMNAT-inhibitor complex
Function / homology
Function and homology information


nicotinate-nucleotide adenylyltransferase / nicotinate-nucleotide adenylyltransferase activity / NAD+ biosynthetic process / ATP binding
Similarity search - Function
Nicotinate/nicotinamide nucleotide adenylyltransferase / Cytidylyltransferase-like / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Chem-JJZ / Probable nicotinate-nucleotide adenylyltransferase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHuang, N. / Eyobo, Y. / Zhang, H.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Complexes of bacterial nicotinate mononucleotide adenylyltransferase with inhibitors: implication for structure-based drug design and improvement.
Authors: Huang, N. / Kolhatkar, R. / Eyobo, Y. / Sorci, L. / Rodionova, I. / Osterman, A.L. / Mackerell, A.D. / Zhang, H.
History
DepositionApr 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 11, 2014Group: Database references
Revision 1.3Sep 6, 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 / 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 / _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: nicotinate-nucleotide adenylyltransferase
B: nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,03710
Polymers44,2212
Non-polymers8168
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-0 kcal/mol
Surface area17170 Å2
MethodPISA
2
A: nicotinate-nucleotide adenylyltransferase
B: nicotinate-nucleotide adenylyltransferase
hetero molecules

A: nicotinate-nucleotide adenylyltransferase
B: nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,07420
Polymers88,4424
Non-polymers1,63316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area13940 Å2
ΔGint-18 kcal/mol
Surface area30330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.586, 97.498, 44.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein nicotinate-nucleotide adenylyltransferase / Deamido-NAD(+) pyrophosphorylase / Deamido-NAD(+) diphosphorylase / Nicotinate mononucleotide ...Deamido-NAD(+) pyrophosphorylase / Deamido-NAD(+) diphosphorylase / Nicotinate mononucleotide adenylyltransferase / NaMN adenylyltransferase


Mass: 22110.451 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: BAMEG_4595, nadD / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: C3L5T6, nicotinate-nucleotide adenylyltransferase
#2: Chemical ChemComp-JJZ / 4-[2-(anthracen-9-ylmethylidene)hydrazino]-N-(3-chlorophenyl)-4-oxobutanamide


Mass: 429.898 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H20ClN3O2
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.16 Å3/Da / Density % sol: 43.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 0.2 M postassium formate 20% PEG3350, pH 7.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 198 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97931 Å
DetectorDetector: CCD / Date: Mar 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 39335 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-3000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 3HFJ

3hfj


Resolution: 1.75→42.709 Å / SU ML: 0.23 / σ(F): 2 / σ(I): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2297 2006 5.13 %Random
Rwork0.1894 ---
obs0.1914 39124 99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.832 Å2 / ksol: 0.359 e/Å3
Refinement stepCycle: LAST / Resolution: 1.75→42.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3051 0 54 308 3413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063217
X-RAY DIFFRACTIONf_angle_d1.0574357
X-RAY DIFFRACTIONf_dihedral_angle_d18.6291186
X-RAY DIFFRACTIONf_chiral_restr0.069469
X-RAY DIFFRACTIONf_plane_restr0.008546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.79380.2941390.24392543X-RAY DIFFRACTION96
1.7938-1.84230.27891620.22812592X-RAY DIFFRACTION99
1.8423-1.89650.25121420.21492581X-RAY DIFFRACTION99
1.8965-1.95770.23441290.20072628X-RAY DIFFRACTION99
1.9577-2.02770.23461520.18732627X-RAY DIFFRACTION99
2.0277-2.10890.2341400.18512660X-RAY DIFFRACTION100
2.1089-2.20490.2441500.18262643X-RAY DIFFRACTION100
2.2049-2.32110.23561700.18332621X-RAY DIFFRACTION100
2.3211-2.46650.25171470.192652X-RAY DIFFRACTION100
2.4665-2.65690.27241280.18892662X-RAY DIFFRACTION100
2.6569-2.92420.22771490.20122695X-RAY DIFFRACTION100
2.9242-3.34730.231180.1872723X-RAY DIFFRACTION100
3.3473-4.21660.19651400.16262743X-RAY DIFFRACTION100
4.2166-42.72190.20991400.18372748X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7150.25920.24961.539-0.44481.4012-0.0937-0.00670.1249-0.00880.0376-0.0243-0.0465-0.22120.0550.1371-0.0359-0.03070.1526-0.0060.11524.4767-28.4128-12.9084
20.84820.16560.10762.2481-0.35270.93270.0063-0.0122-0.0421-0.118-0.0792-0.31020.1060.12120.07350.1258-0.01880.01020.16750.030.173520.6737-47.2068-15.9269
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 188
2X-RAY DIFFRACTION2chain BB1 - 189

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