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Basic information

Entry
Database: PDB / ID: 2wek
TitleCrystal structure of the human MGC45594 gene product in complex with diclofenac
ComponentsZINC-BINDING ALCOHOL DEHYDROGENASE DOMAIN-CONTAINING PROTEIN 2
KeywordsOXIDOREDUCTASE / NADP / DRUG METABOLISM / MEDIUM-CHAIN DEHYDROGENASE/REDUCTASE
Function / homology
Function and homology information


13,14-dehydro-15-oxoprostaglandin 13-reductase / 13-prostaglandin reductase activity / 15-oxoprostaglandin 13-oxidase activity / negative regulation of fat cell differentiation / peroxisome / zinc ion binding
Similarity search - Function
Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase ...Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / PHOSPHATE ION / Prostaglandin reductase 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsShafqat, N. / Yue, W.W. / Ugochukwu, E. / Niesen, F. / Smee, C. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Bountra, C. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of the Human Mgc45594 Gene Product in Complex with Diclofenac
Authors: Shafqat, N. / Yue, W.W. / Niesen, F. / Oppermann, U.
History
DepositionMar 31, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ZINC-BINDING ALCOHOL DEHYDROGENASE DOMAIN-CONTAINING PROTEIN 2
B: ZINC-BINDING ALCOHOL DEHYDROGENASE DOMAIN-CONTAINING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,11422
Polymers72,5012
Non-polymers4,61320
Water7,080393
1
A: ZINC-BINDING ALCOHOL DEHYDROGENASE DOMAIN-CONTAINING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,62112
Polymers36,2511
Non-polymers2,37011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ZINC-BINDING ALCOHOL DEHYDROGENASE DOMAIN-CONTAINING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,49310
Polymers36,2511
Non-polymers2,2439
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.834, 51.572, 75.716
Angle α, β, γ (deg.)94.61, 91.54, 101.72
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A26 - 36
2113B26 - 36
1212A40 - 314
2212B40 - 314
1314A320 - 360
2314B320 - 360

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ZINC-BINDING ALCOHOL DEHYDROGENASE DOMAIN-CONTAINING PROTEIN 2 / MGC45594


Mass: 36250.730 Da / Num. of mol.: 2 / Fragment: RESIDUES 33-371
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8N4Q0, Oxidoreductases

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Non-polymers , 6 types, 413 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-DIF / 2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID / DICLOFENAC / Diclofenac


Mass: 296.149 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C14H11Cl2NO2 / Comment: antiinflammatory, medication*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.26 Å3/Da / Density % sol: 45.61 % / Description: NONE
Crystal growDetails: 25% 1,2 PROPANDIOL, 10% GLYCEROL, 0.1M NA/K-PO4 PH 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: OSMIC
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→28.5 Å / Num. obs: 54443 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.3
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.8 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.5.0089refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C0C

2c0c


Resolution: 1.9→75.38 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.988 / SU ML: 0.11 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2568 5.1 %RANDOM
Rwork0.165 ---
obs0.168 47367 91.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.56 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å2-1.55 Å20.03 Å2
2--2.5 Å20.22 Å2
3----1.52 Å2
Refinement stepCycle: LAST / Resolution: 1.9→75.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4985 0 291 393 5669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225390
X-RAY DIFFRACTIONr_bond_other_d0.0010.023493
X-RAY DIFFRACTIONr_angle_refined_deg1.5162.0447346
X-RAY DIFFRACTIONr_angle_other_deg0.9353.0048450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9175683
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.6124.405168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02315809
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6981515
X-RAY DIFFRACTIONr_chiral_restr0.0860.2837
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215946
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02977
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9433379
X-RAY DIFFRACTIONr_mcbond_other0.79231392
X-RAY DIFFRACTIONr_mcangle_it2.72855434
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.58872011
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.056111910
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1667tight positional0.120.05
2B1667tight positional0.120.05
1A2216medium positional0.230.5
2B2216medium positional0.230.5
1A76loose positional0.155
2B76loose positional0.155
1A1667tight thermal0.880.5
2B1667tight thermal0.880.5
1A2216medium thermal0.982
2B2216medium thermal0.982
1A76loose thermal1.0110
2B76loose thermal1.0110
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 169 -
Rwork0.339 2894 -
obs--75.44 %
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)
14.45051.77610.2612.0583-0.26411.2512-0.10420.27530.3576-0.13090.06940.0737-0.28510.02780.03480.0956-0.003-0.00370.08380.00380.0766-13.17938.6994-5.6113
21.11660.7094-0.2322.2701-0.64531.8696-0.0359-0.0253-0.1858-0.0266-0.0064-0.10.17170.05930.04230.01950.0151-0.00230.0343-0.02590.0645-15.2609-14.048.0794
31.8663-0.65461.04552.9959-3.83746.50560.0156-0.0533-0.04880.13960.17840.3204-0.0842-0.4594-0.1940.01670.00110.02260.0568-0.01960.0707-29.1376-9.15849.8804
42.51450.4705-1.24911.3086-0.42292.1860.0047-0.05110.06810.0338-0.0027-0.0723-0.01250.1122-0.0020.02310.0118-0.02550.0179-0.0120.0327-15.0361-5.931614.0328
51.42880.1772-1.97535.2176-2.43835.8834-0.21490.5493-0.2076-0.76410.0653-0.22370.4737-0.16970.14960.1462-0.11530.06150.369-0.13330.0766-13.7791-7.285-11.1846
63.4099-1.77642.38553.6867-2.67359.4963-0.0424-0.3579-0.31260.26990.19870.25060.8038-0.9269-0.15630.2854-0.1590.03040.1901-0.00470.2164-49.3225-17.8273-31.0372
71.8723-0.13240.68532.0285-1.12145.14670.0438-0.0587-0.39480.19990.0138-0.10190.76620.1333-0.05760.2150.00460.01970.08210.00170.1802-38.196-14.5402-28.5816
81.24740.378-0.52271.4592-0.38562.78580.0132-0.01940.12530.07470.0068-0.0078-0.28640.0678-0.02010.03780.0095-0.00640.0493-0.01790.0467-34.07866.5997-39.9961
91.15210.3111-1.25580.8543-0.46773.75120.0036-0.0991-0.00290.1369-0.0090.03190.0048-0.09550.00540.03090.0138-0.00630.0611-0.00490.0909-31.95980.7082-40.0264
104.392.1454-1.88826.5697-2.18196.64990.1335-0.27230.08160.2690.04430.48190.0607-0.7875-0.17780.0492-0.00050.0270.2013-0.00420.0742-49.4823-2.088-29.3175
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 119
2X-RAY DIFFRACTION2A120 - 250
3X-RAY DIFFRACTION3A251 - 277
4X-RAY DIFFRACTION4A278 - 322
5X-RAY DIFFRACTION5A323 - 362
6X-RAY DIFFRACTION6B21 - 53
7X-RAY DIFFRACTION7B54 - 119
8X-RAY DIFFRACTION8B120 - 270
9X-RAY DIFFRACTION9B271 - 331
10X-RAY DIFFRACTION10B332 - 362

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