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Open data


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Basic information

Entry
Database: PDB / ID: 4elh
TitleStructure-activity relationship guides enantiomeric preference among potent inhibitors of B. anthracis dihydrofolate reductase
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / dihydrofolate reductase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / metal ion binding
Similarity search - Function
Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-53I / Chem-53J / Dihydrofolate reductase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.103 Å
AuthorsBourne, C.R. / Barrow, W.W.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Structure-activity relationship for enantiomers of potent inhibitors of B. anthracis dihydrofolate reductase.
Authors: Bourne, C.R. / Wakeham, N. / Nammalwar, B. / Tseitin, V. / Bourne, P.C. / Barrow, E.W. / Mylvaganam, S. / Ramnarayan, K. / Bunce, R.A. / Berlin, K.D. / Barrow, W.W.
History
DepositionApr 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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: Dihydrofolate reductase
H: Dihydrofolate reductase
C: Dihydrofolate reductase
B: Dihydrofolate reductase
G: Dihydrofolate reductase
F: Dihydrofolate reductase
D: Dihydrofolate reductase
E: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,01533
Polymers156,9248
Non-polymers5,09125
Water23,0591280
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1904
Polymers19,6151
Non-polymers5743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
H: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1904
Polymers19,6151
Non-polymers5743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1904
Polymers19,6151
Non-polymers5743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1904
Polymers19,6151
Non-polymers5743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
G: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1904
Polymers19,6151
Non-polymers5743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1904
Polymers19,6151
Non-polymers5743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
D: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6885
Polymers19,6151
Non-polymers1,0734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
E: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1904
Polymers19,6151
Non-polymers5743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.350, 136.034, 168.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 8 molecules AHCBGFDE

#1: Protein
Dihydrofolate reductase /


Mass: 19615.453 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: A thrombin cut site was engineered between the C-terminus and the 6 x His tag
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: BAS2083, BA_2237, dfrA, DHFR, GBAA_2237 / Plasmid: pCR-T7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q81R22, dihydrofolate reductase

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Non-polymers , 5 types, 1305 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-53I / (2E)-3-{5-[(2,4-diaminopyrimidin-5-yl)methyl]-2,3-dimethoxyphenyl}-1-[(1R)-1-(2-methylprop-1-en-1-yl)phthalazin-2(1H)-y l]prop-2-en-1-one / (R,E)-3-(5-((2,4-diaminopyrimidin-5-yl)methyl)-2,3-dimethoxyphenyl)-1-(1-(2-methylprop-1-en-1-yl)phthalazin-2(1H)-yl)pr op-2-en-1-one


Mass: 498.576 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C28H30N6O3
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-53J / (2E)-3-{5-[(2,4-diaminopyrimidin-5-yl)methyl]-2,3-dimethoxyphenyl}-1-[(1S)-1-(2-methylprop-1-en-1-yl)phthalazin-2(1H)-y l]prop-2-en-1-one / (S,E)-3-(5-((2,4-diaminopyrimidin-5-yl)methyl)-2,3-dimethoxyphenyl)-1-(1-(2-methylprop-1-en-1-yl)phthalazin-2(1H)-yl)pr op-2-en-1-one


Mass: 498.576 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H30N6O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1280 / 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: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 16-22% PEG 3350, 0.2M CaCl2, 0.1M MES, +/- 3% glycerol , pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 1.38 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 2.1→43.8 Å / Num. obs: 90525 / % possible obs: 98.5 % / Redundancy: 4.4 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 24.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FL8

3fl8


Resolution: 2.103→43.784 Å / SU ML: 0.69 / σ(F): 1.34 / Phase error: 27.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2519 1994 2.21 %
Rwork0.1935 --
obs0.1948 90400 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.635 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.2144 Å2-0 Å2-0 Å2
2---0.8737 Å20 Å2
3----8.3407 Å2
Refinement stepCycle: LAST / Resolution: 2.103→43.784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11034 0 349 1280 12663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711698
X-RAY DIFFRACTIONf_angle_d1.10615841
X-RAY DIFFRACTIONf_dihedral_angle_d16.7374412
X-RAY DIFFRACTIONf_chiral_restr0.071601
X-RAY DIFFRACTIONf_plane_restr0.0052019
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1034-2.1560.2721350.21875992X-RAY DIFFRACTION95
2.156-2.21430.33731400.22666256X-RAY DIFFRACTION98
2.2143-2.27950.3691360.26596057X-RAY DIFFRACTION95
2.2795-2.35310.3171420.22676239X-RAY DIFFRACTION98
2.3531-2.43710.35561400.23226262X-RAY DIFFRACTION98
2.4371-2.53470.2981420.21936245X-RAY DIFFRACTION99
2.5347-2.65010.30331410.21776262X-RAY DIFFRACTION99
2.6501-2.78980.28021420.20646306X-RAY DIFFRACTION99
2.7898-2.96450.26011440.19886381X-RAY DIFFRACTION99
2.9645-3.19330.26351440.19666367X-RAY DIFFRACTION100
3.1933-3.51460.25211450.20146419X-RAY DIFFRACTION100
3.5146-4.02280.21781460.18086452X-RAY DIFFRACTION99
4.0228-5.06710.17081450.1366474X-RAY DIFFRACTION99
5.0671-43.79390.22951520.1916694X-RAY DIFFRACTION99
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)
10.15060.3234-0.59631.8938-0.49473.5710.1156-0.06330.0158-0.0033-0.02140.0423-0.17410.3202-0.10080.1232-0.0314-0.0070.2160.00880.21316.345-33.0748-4.3235
22.08510.2477-0.50724.76211.92923.10520.1854-0.1020.2903-0.53880.0842-0.458-0.55080.5041-0.20760.3116-0.06470.04270.25310.00620.244420.3928-24.1387-15.0964
30.8078-0.2031-0.21181.0416-0.22241.37170.04110.0157-0.1005-0.14570.02160.17040.0559-0.2207-0.05930.1171-0.02-0.03690.20130.00870.209510.3403-40.5567-6.6882
42.97650.8731.42741.82770.22823.57180.152-0.0172-0.1144-0.2413-0.0426-0.07940.7945-0.2954-0.08420.3134-0.0319-0.01960.1590.01520.22697.47-2.48882.6428
50.4782-0.02080.05461.4948-1.49233.2668-0.0130.0737-0.0796-0.0927-0.0435-0.04560.26120.15940.05610.1390.00250.02540.1902-0.01110.210212.7759-1.94818.5582
62.4918-5.2191-5.86252.01521.99262.00650.08080.1659-0.6874-0.2353-0.0742-0.69710.74030.06120.04030.44070.05850.08110.4514-0.19410.56633.159719.838722.1284
71.45420.0389-0.55931.33570.24473.6664-0.0831-0.0827-0.11890.28990.08360.01180.3408-0.21930.00370.35030.0271-0.02380.16840.0110.175419.3242-38.177339.2262
81.5235-0.00090.93751.9060.03423.1334-0.033-0.13090.11360.4184-0.00510.1771-0.185-0.3170.03360.24990.0270.03180.1425-0.01140.205513.9113-35.839429.1127
91.72360.297-1.62481.11630.78383.3995-0.18140.0473-0.2436-0.037-0.002-0.03180.08860.04670.15420.37680.0822-0.0590.1717-0.01560.207630.4996-41.804736.3328
100.2735-0.29920.31971.5051-0.36134.5099-0.07-0.04180.2350.2087-0.0435-0.1955-1.04530.56680.060.4103-0.0948-0.08780.3237-0.01550.265913.831436.6126-5.4716
110.5928-0.62020.2511.7176-0.75093.6201-0.0444-0.02630.0634-0.1369-0.0757-0.0487-0.6577-0.05450.11610.2756-0.0317-0.0520.1681-0.01060.206610.262133.5213-10.0749
121.00423.20182.60519.78928.01146.52760.00980.8414-0.59460.2027-0.50320.68190.2067-1.19050.42850.53880.0013-0.15070.6669-0.24210.48214.195914.231-21.9984
131.84690.75210.85121.8139-0.57513.08930.0781-0.11020.07380.1576-0.12420.1839-0.6456-0.35820.02160.37780.07-0.00260.2061-0.0370.203213.057629.989537.573
141.14270.78830.53211.00480.73713.2704-0.05340.06270.07640.0116-0.04030.0811-0.4627-0.36210.07740.40220.0759-0.03360.1786-0.0140.189613.885829.22332.4102
152.0146-5.5599-9.60372.33254.84342.0059-0.40340.0252-0.2605-0.15920.1822-0.03190.475-0.53350.29170.98980.05490.08990.4102-0.06180.480236.825920.938919.3922
161.22640.24270.80560.1040.11392.5901-0.0101-0.17540.0899-0.0602-0.02940.1729-0.365-0.370.01680.25620.04370.02420.2859-0.05810.2643-20.5765-3.074338.4694
170.79420.56691.00430.91440.4793.378-0.0431-0.01650.0338-0.0895-0.04210.1054-0.0228-0.20140.08180.13160.02620.00590.1742-0.04650.1899-17.1576-5.90232.9562
182.0132.9582-2.09226.343-1.82352.0116-0.1698-0.2985-0.80041.0199-0.14731.04170.5573-0.66350.39710.31320.010.09780.3688-0.01680.44754.0944-14.513517.8563
190.95570.37750.20561.5077-0.47863.0606-0.08550.09490.17610.255-0.0724-0.102-0.79090.2240.14480.3392-0.0447-0.09640.22320.00910.2505-19.68685.229-5.6569
200.7986-0.65380.821.1863-0.73993.8353-0.05710.06030.0679-0.0266-0.13320.0256-0.2263-0.07090.1930.1402-0.0467-0.03370.186-0.00530.2132-22.7162-2.3726-8.0916
211.9484.14335.97912.01651.99252.00990.2835-0.0752-0.2180.1984-0.4582-0.1587-0.654-0.46650.12580.5479-0.0913-0.10860.3903-0.0710.383-28.3031-22.2416-22.6201
222.8502-0.40591.2831.9785-2.22295.2518-0.2986-0.18970.22570.3256-0.142-0.4696-0.66710.67510.38170.2408-0.0371-0.05440.26910.02920.278121.553-2.858950.9144
233.56940.0022-0.57761.68890.11294.652-0.0965-0.3793-0.19280.0837-0.09190.05450.36-0.09020.19740.1994-0.00480.00590.1630.00180.18617.6567-6.687545.0113
242.01324.7883-8.08552.1318-4.43692.0033-0.0470.2130.0654-0.24060.1698-0.7870.71410.8008-0.07520.73120.05680.36430.52070.12610.5742-2.7284-12.575966.6741
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:43)
2X-RAY DIFFRACTION2(chain A and resid 44:101)
3X-RAY DIFFRACTION3(chain A and resid 102:166)
4X-RAY DIFFRACTION4(chain B and resid 1:24)
5X-RAY DIFFRACTION5(chain B and resid 25:160)
6X-RAY DIFFRACTION6(chain B and resid 161:166)
7X-RAY DIFFRACTION7(chain C and resid 1:36)
8X-RAY DIFFRACTION8(chain C and resid 37:126)
9X-RAY DIFFRACTION9(chain C and resid 127:166)
10X-RAY DIFFRACTION10(chain D and resid 1:60)
11X-RAY DIFFRACTION11(chain D and resid 61:158)
12X-RAY DIFFRACTION12(chain D and resid 159:166)
13X-RAY DIFFRACTION13(chain E and resid 1:47)
14X-RAY DIFFRACTION14(chain E and resid 48:160)
15X-RAY DIFFRACTION15(chain E and resid 161:166)
16X-RAY DIFFRACTION16(chain F and resid 1:58)
17X-RAY DIFFRACTION17(chain F and resid 59:161)
18X-RAY DIFFRACTION18(chain F and resid 162:166)
19X-RAY DIFFRACTION19(chain G and resid 1:70)
20X-RAY DIFFRACTION20(chain G and resid 71:160)
21X-RAY DIFFRACTION21(chain G and resid 161:166)
22X-RAY DIFFRACTION22(chain H and resid 1:126)
23X-RAY DIFFRACTION23(chain H and resid 127:160)
24X-RAY DIFFRACTION24(chain H and resid 161:166)

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