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- PDB-7ere: Crystal structure of human Biliverdin IX-beta reductase B with Py... -

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Basic information

Entry
Database: PDB / ID: 7ere
TitleCrystal structure of human Biliverdin IX-beta reductase B with Pyrantel Pamoate (PPA)
ComponentsFlavin reductase (NADPH)
KeywordsOXIDOREDUCTASE / platelets / Biliverdin reductase B / BLVRB / inhibitors / NADP / Pyrantel Pamoate
Function / homology
Function and homology information


biliberdin reductase NAD+ activity / biliverdin reductase (NADPH) activity / biliverdin reductase / biliverdin reductase (NAD(P)H) activity / flavin reductase (NADPH) / riboflavin reductase (NADPH) activity / heme catabolic process / Heme degradation / terminal bouton / Cytoprotection by HMOX1 ...biliberdin reductase NAD+ activity / biliverdin reductase (NADPH) activity / biliverdin reductase / biliverdin reductase (NAD(P)H) activity / flavin reductase (NADPH) / riboflavin reductase (NADPH) activity / heme catabolic process / Heme degradation / terminal bouton / Cytoprotection by HMOX1 / intracellular membrane-bounded organelle / extracellular exosome / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
NAD(P)H-binding / NAD(P)-binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-JBR / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Flavin reductase (NADPH)
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGriesinger, C. / Lee, D. / Ryu, K.S. / Kim, M. / Ha, J.H.
CitationJournal: J.Med.Chem. / Year: 2022
Title: Repositioning Food and Drug Administration-Approved Drugs for Inhibiting Biliverdin IX beta Reductase B as a Novel Thrombocytopenia Therapeutic Target.
Authors: Kim, M. / Ha, J.H. / Choi, J. / Kim, B.R. / Gapsys, V. / Lee, K.O. / Jee, J.G. / Chakrabarti, K.S. / de Groot, B.L. / Griesinger, C. / Ryu, K.S. / Lee, D.
History
DepositionMay 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flavin reductase (NADPH)
B: Flavin reductase (NADPH)
C: Flavin reductase (NADPH)
D: Flavin reductase (NADPH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,34619
Polymers89,1464
Non-polymers5,20015
Water14,268792
1
A: Flavin reductase (NADPH)
B: Flavin reductase (NADPH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1259
Polymers44,5732
Non-polymers2,5527
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-45 kcal/mol
Surface area17220 Å2
MethodPISA
2
C: Flavin reductase (NADPH)
D: Flavin reductase (NADPH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,22110
Polymers44,5732
Non-polymers2,6488
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-58 kcal/mol
Surface area17120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.982, 117.381, 81.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Flavin reductase (NADPH) / FR / Biliverdin reductase B / BVR-B / Biliverdin-IX beta-reductase / Green heme-binding protein / ...FR / Biliverdin reductase B / BVR-B / Biliverdin-IX beta-reductase / Green heme-binding protein / GHBP / NADPH-dependent diaphorase / NADPH-flavin reductase / FLR


Mass: 22286.494 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BLVRB, FLR / Production host: Escherichia coli (E. coli)
References: UniProt: P30043, flavin reductase (NADPH), biliverdin reductase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-JBR / 4-[(3-carboxy-2-oxidanyl-naphthalen-1-yl)methyl]-3-oxidanyl-naphthalene-2-carboxylic acid / Pamoic acid


Mass: 388.370 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H16O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 792 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.9-2.0M Ammonium sulfate, 0.1M Bis-tris(pH 6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.6→47.72 Å / Num. obs: 107048 / % possible obs: 99.63 % / Redundancy: 10.2 % / Biso Wilson estimate: 15.42 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09368 / Net I/σ(I): 11.92
Reflection shellResolution: 1.6→1.657 Å / Rmerge(I) obs: 0.3682 / Num. unique obs: 10523 / CC1/2: 0.927

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Processing

Software
NameVersionClassification
HKL-20001.16_3549data collection
HKL-20001.16_3549data scaling
PHENIXmodel building
PHENIX1.19.2refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HE5
Resolution: 1.6→47.72 Å / SU ML: 0.1718 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 20.1875
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.198 1999 1.87 %
Rwork0.1709 104890 -
obs0.1714 106889 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.39 Å2
Refinement stepCycle: LAST / Resolution: 1.6→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6232 0 343 792 7367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00886839
X-RAY DIFFRACTIONf_angle_d1.0429401
X-RAY DIFFRACTIONf_chiral_restr0.06011079
X-RAY DIFFRACTIONf_plane_restr0.00651182
X-RAY DIFFRACTIONf_dihedral_angle_d10.08815360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.27821440.24917386X-RAY DIFFRACTION98.94
1.64-1.680.26211380.2277393X-RAY DIFFRACTION99.68
1.68-1.730.25251360.21557402X-RAY DIFFRACTION99.64
1.73-1.790.23141450.19587439X-RAY DIFFRACTION99.71
1.79-1.850.19861430.1827409X-RAY DIFFRACTION99.67
1.85-1.930.21841400.17087451X-RAY DIFFRACTION99.88
1.93-2.020.18711390.16597451X-RAY DIFFRACTION99.75
2.02-2.120.21021450.1627485X-RAY DIFFRACTION99.9
2.12-2.260.18221400.15717462X-RAY DIFFRACTION99.82
2.26-2.430.18221470.15567508X-RAY DIFFRACTION99.84
2.43-2.670.19761400.15997540X-RAY DIFFRACTION99.93
2.67-3.060.1951470.16767554X-RAY DIFFRACTION99.91
3.06-3.860.1711470.15397631X-RAY DIFFRACTION99.92
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.00270774212-0.935710729993-0.2770156754442.19042918693-0.6231097782560.878592880229-0.408012280735-0.1165486760150.2540326923380.2536780955920.150810207039-0.326438884417-0.232958827170.2849370354590.09514181381110.1235636422320.0136027986428-0.01609772206290.178594956449-0.0157184684650.13707350877315.8344286387-23.274990905920.8055957159
20.82197465418-0.138874975696-0.2194760140590.759192573929-0.05614938194011.57822570589-0.076831788348-0.07434690257890.08626821646510.01782640612660.0213613032756-0.104568423089-0.4880216807050.2261756548430.02718624124520.163897847303-0.040530165423-0.02836507922120.115104397884-0.001842914676760.11080556221911.8599415093-17.891838414521.6421013351
31.664711455410.1950532628210.1149934528290.9010243345980.3265123872521.75592078142-0.1059379327120.1893707554350.22192910238-0.1553675553030.006099250257490.0497994819339-0.4373987175390.05489098212160.06565050626260.1291970391280.00619761403384-0.02346682510950.1109124710740.02202372336210.1184719978937.25670110774-21.429077811911.519138671
44.40772227478-1.40248860591-0.2275705410561.369276354160.1115255541080.9397317972130.05807100154710.21177057501-0.0339643775685-0.0876559382934-0.0437770333708-0.0406008007266-0.02961420443680.0838545843537-0.04155304427190.07876992430480.005157075314670.005552543430010.128377229228-0.003432503981180.09993749017718.57538627419-33.903784923810.2420172268
51.32834134792-0.3024618150490.1745595683420.8058653450830.1865752700161.39676623069-0.0322609672925-0.0470850358005-0.09333245346170.05205351504870.01936908911990.0594788096050.0727080187879-0.1649332586290.02415966489930.06185475999030.01806090384430.003918650935610.1077160440370.003430995150220.110630896265-2.02206574475-34.399757235120.784273033
61.070932244690.461417337252-0.07270529709033.26783678794-0.21519186170.9113022267040.111117958393-0.1383353666710.0552628802692-0.0941688495249-0.1668815486870.0100526415941-0.206907543351-0.4034984028250.03204385613440.1377058915090.06193465113240.008183118486720.134553837742-0.0152690750170.0637609236467-0.940509479836-26.760637548234.8304382913
70.8324180812440.2191757989540.1320429807851.27830370798-0.02435708886261.08680172336-0.0149498033326-0.126173732037-0.0336393949710.172905027686-0.0044472078118-0.0355392147486-0.07846087120150.02364720778360.0220324520190.1217348289420.0316241949288-0.001487991567110.1390193087420.00205250779730.09708435713965.13060700592-27.443597390231.6884883326
80.744106283716-0.434872154965-0.3040563064232.55886027811-0.7958285488361.52931690052-0.056436537739-0.1099942724470.13743151687-0.341713663628-0.0405248082746-0.4122959834950.2224341266130.3069662028660.05745934607090.403575164975-0.06447428352260.05825397629810.0897889399440.02447591902410.2139308203490.518762093225-61.11371439262.79794019455
90.586061731269-0.1230876065630.7221325404052.55579811885-0.7673827926541.009598738550.04718619791310.00708869168923-0.0132569106345-0.296394364347-0.04653386760350.07553699941810.488670761462-0.2129229530340.02626382988410.316216367817-0.08636825167930.0119203614820.155801361229-0.01742976763650.130157276531-9.09089928427-51.2923460024-3.49411133771
101.21235896235-0.3532940102830.1802726023062.14491063922-0.5870892504671.40465200412-0.0349111376091-0.197147964074-0.002816262067760.1295315579080.1394372098040.2614848298250.235167406918-0.425524110586-0.06573280952370.208996106137-0.07620231645710.02013445308120.26170678278-0.01146076329320.182544983549-13.9178136756-50.33603056538.05863264085
110.5121537046540.4581099199560.4449650714662.22502730055-0.5750413228540.890875193222-0.3979988133440.224544388409-0.196791410492-0.2649604118330.19073127798-0.2821247872610.2665551517910.3836999527090.09919754846580.0751384233437-0.01771394138560.02763522224230.216363410649-0.02112073858650.11020333573415.6064098069-35.6353709696-20.8654935926
120.7750217037910.141419824548-0.04984550812360.8318787293410.1842283124061.75089049473-0.0533068595399-0.0402514399344-0.0779074252398-0.03744257046950.0662950821717-0.08648213512790.2307884896740.250034604456-0.02411228502860.0862166763370.02135231224970.0116692523670.0882708151578-0.003352210434720.11109239827611.3091911513-40.9162015994-21.8057730117
132.60471655849-0.121886586244-1.152023203930.2565860054410.8051737718913.79763420383-0.1560893906080.0973708462006-0.7748183056010.3831791332040.08239898780720.1981591139161.53892430685-0.3316011777580.1026835176550.4117761471310.03854283910780.0424625227970.2083613721480.0830721306430.3363074108318.0380507656-46.9792077555-12.7887752457
141.25033901923-0.04079788403750.1670039235791.297053909490.07704970977640.506397361927-0.222177311409-0.4468424412110.156324860820.2084828627120.198252582067-0.02013906599970.2115153379560.1526427156040.07568891328660.09795075599730.0416048850433-0.0006554435396430.1529991046690.02080347944780.08007885142359.65931860391-36.5844242503-6.9022204283
151.60916313427-0.895097151281-1.064865748162.742126683310.8764966155751.50185964093-0.230998540881-0.0816956204432-0.1468207512841.058153368810.2294554391720.02933775752390.2017489562910.490570998061-0.0848904901842-0.200079838504-0.0419307232234-0.05129533878010.151854332896-0.0170871014160.092943524459414.5330252886-31.4364954537-11.9563915241
161.48596905186-1.04715483782-0.8277100113070.7456410825830.5182312347460.624610829006-0.12546675410.036117035086-0.2139819769930.0207375211964-0.0379299639770.2931020445070.00288406582018-0.1076939100480.09845561952760.0819404847171-0.01803592475660.009392826118780.119452755575-0.0006567365389840.138964342076-5.85177584256-33.6990841914-12.9927749773
174.616615029781.223054010120.1998750347461.586950269290.1684986802791.17023684973-0.0866907281979-0.1497837379910.1391037169250.02364853030230.1111543708430.000244229669321-0.07050898654190.142226785087-0.07742404597220.0885247649301-0.000399693825002-0.005316593800970.127859721597-0.0166588133740.115043360768.66859770356-24.9032868602-10.215239189
181.475938389870.444130112498-0.2263081966990.8946852548280.2997722865481.638253466950.03597036087320.3597086288020.160460075566-0.06955976509850.008273938226350.0882123202726-0.163349564868-0.132010873764-0.01272807907520.083959987707-0.0114890826076-0.0034206705360.1197928808020.02440224787710.111657309493-1.98587919681-23.5923620887-22.9021488563
192.707043939840.30560698470.02798509927280.7355428681530.297719368760.811871549859-0.0821123514203-0.0614713394989-0.0437713620484-0.05042656317780.0497093098391-0.0788771981269-0.146999712552-0.1032144009220.005074060719350.08866144746070.0102904966983-0.001522564942660.106471934984-0.008181638714440.107684772012-4.38400866862-22.6873098036-16.5537956793
200.344633582233-0.3737169672290.2985063484830.6263691427430.1519843786421.535974453930.01944333779270.09950585330020.0637707870469-0.2170644739630.01470890311680.0282775218236-0.121152911166-0.0231473171566-0.06070535280340.0698282526787-0.02403485728410.01163011555530.0742705160321-0.006676521553530.07764978600012.67993275998-26.7328526085-24.7546470891
210.94639548688-0.3569918348930.01791345425823.58983996228-0.3252785714651.154489861130.001566991777610.0334506371762-0.0225099080827-0.01599920578890.001570369763150.189513234109-0.0160620615817-0.218846107028-0.008052187006080.114710471841-0.0269264533977-0.01417293695420.128079008053-0.006794283950170.0896160457172-1.27643018788-31.7791772997-34.5928125026
221.902348792240.7003594573650.3910785776441.200300207070.3156926594360.728379079769-0.224167339650.06442412590780.157435595031-0.3046654440160.132065744596-0.02862270048060.03044161122430.05847872618370.02648241382250.10284840157-0.0413804717994-0.002245339192350.103433056353-0.00485527793390.1079256408815.94563277551-34.567503638-29.8098843724
231.17091579627-0.158042116995-0.02599805285961.67251499878-0.3434470396150.555252392281-0.06914853363750.1843614900980.0546243986386-0.3280214313870.04271673298260.0780654816429-0.1594492948440.0633579442843-0.0365147723910.136128320852-0.0499151141050.01864980518150.1505402119940.01399197603730.08313655668074.04315492446-27.7550640111-33.4619557651
241.163598229230.6699098066940.3847873225611.95318584847-0.2361839549831.39244009313-0.0143797020372-0.0154112605568-0.04598842342040.147327506353-0.018393089719-0.227333056419-0.1427982290990.1642890440130.04216576140660.2484960953950.0468936096811-0.00804731979130.09778841223040.01621320216770.1581917768481.402785130242.78717114631-2.83229672583
250.6764162220180.622261709922-0.3943881145472.96900322818-0.5405027617560.9571964837090.0472358104354-0.0203423593370.02095408940490.2640026490850.01167248837750.234549661928-0.295053120696-0.234057002895-0.03652466265810.2058595032780.08421745422360.02029443749930.154302748854-0.00125097925540.131301372347-9.24809700932-9.213406663783.41923312687
262.25203902750.338364198824-0.366103161582.44881071531-0.1449280963591.33824351664-0.1119523677270.342594224268-0.0489917626018-0.2730059898830.1226440578960.424501661787-0.156865719287-0.3535174029890.01681182925540.2443193649270.0678064004097-0.03716560828430.2244200687480.007178163073270.216515985824-13.7807021702-5.06956731115-11.9684190841
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 13 )
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 34 )
3X-RAY DIFFRACTION3chain 'A' and (resid 35 through 85 )
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 101 )
5X-RAY DIFFRACTION5chain 'A' and (resid 102 through 155 )
6X-RAY DIFFRACTION6chain 'A' and (resid 156 through 174 )
7X-RAY DIFFRACTION7chain 'A' and (resid 175 through 206 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 57 )
9X-RAY DIFFRACTION9chain 'B' and (resid 58 through 122 )
10X-RAY DIFFRACTION10chain 'B' and (resid 123 through 206 )
11X-RAY DIFFRACTION11chain 'C' and (resid 0 through 13 )
12X-RAY DIFFRACTION12chain 'C' and (resid 14 through 34 )
13X-RAY DIFFRACTION13chain 'C' and (resid 35 through 48 )
14X-RAY DIFFRACTION14chain 'C' and (resid 49 through 57 )
15X-RAY DIFFRACTION15chain 'C' and (resid 58 through 73 )
16X-RAY DIFFRACTION16chain 'C' and (resid 74 through 85 )
17X-RAY DIFFRACTION17chain 'C' and (resid 86 through 101 )
18X-RAY DIFFRACTION18chain 'C' and (resid 102 through 122 )
19X-RAY DIFFRACTION19chain 'C' and (resid 123 through 142 )
20X-RAY DIFFRACTION20chain 'C' and (resid 143 through 155 )
21X-RAY DIFFRACTION21chain 'C' and (resid 156 through 174 )
22X-RAY DIFFRACTION22chain 'C' and (resid 175 through 190 )
23X-RAY DIFFRACTION23chain 'C' and (resid 191 through 206 )
24X-RAY DIFFRACTION24chain 'D' and (resid 1 through 57 )
25X-RAY DIFFRACTION25chain 'D' and (resid 58 through 142 )
26X-RAY DIFFRACTION26chain 'D' and (resid 143 through 206 )

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