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- PDB-7erc: Crystal structure of human Biliverdin IX-beta reductase B with De... -

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Basic information

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


biliberdin reductase (NAD+) activity / biliverdin reductase (NADP+) activity / biliverdin reductase [NAD(P)+] activity / flavin reductase (NADPH) / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / megakaryocyte differentiation / riboflavin reductase (NADPH) activity / heme catabolic process ...biliberdin reductase (NAD+) activity / biliverdin reductase (NADP+) activity / biliverdin reductase [NAD(P)+] activity / flavin reductase (NADPH) / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / megakaryocyte differentiation / riboflavin reductase (NADPH) activity / heme catabolic process / Heme degradation / negative regulation of insulin receptor signaling pathway / Cytoprotection by HMOX1 / intracellular membrane-bounded organelle / extracellular exosome / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
NAD(P)H-binding / NAD(P)-binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-JBL / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Flavin reductase (NADPH)
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,2536
Polymers44,2972
Non-polymers1,9564
Water5,873326
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-11 kcal/mol
Surface area17320 Å2
Unit cell
Length a, b, c (Å)81.880, 117.503, 41.765
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-547-

HOH

21A-653-

HOH

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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: 22148.350 Da / Num. of mol.: 2
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


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-JBL / 4-[3,5-bis(2-hydroxyphenyl)-1,2,4-triazol-1-yl]benzoic acid


Mass: 373.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H15N3O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.27 Å3/Da / Density % sol: 45.76 %
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: 11C / 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: 1.5→47.73 Å / Num. obs: 64875 / % possible obs: 99.49 % / Redundancy: 10 % / Biso Wilson estimate: 15.93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09644 / Net I/σ(I): 14.58
Reflection shellResolution: 1.5→1.556 Å / Rmerge(I) obs: 0.4497 / Num. unique obs: 6334 / CC1/2: 0.737

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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

1he5


Resolution: 1.5→47.73 Å / SU ML: 0.1633 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 20.0929
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2274 2000 3.08 %
Rwork0.1951 62875 -
obs0.1961 64875 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.38 Å2
Refinement stepCycle: LAST / Resolution: 1.5→47.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3106 0 129 326 3561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143329
X-RAY DIFFRACTIONf_angle_d1.41424562
X-RAY DIFFRACTIONf_chiral_restr0.0826533
X-RAY DIFFRACTIONf_plane_restr0.0091575
X-RAY DIFFRACTIONf_dihedral_angle_d11.42152647
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.27151400.25164377X-RAY DIFFRACTION97.98
1.54-1.580.29151380.23824367X-RAY DIFFRACTION98.71
1.58-1.630.25691410.23384443X-RAY DIFFRACTION99.39
1.63-1.680.24191420.2254434X-RAY DIFFRACTION99.54
1.68-1.740.29311410.21794454X-RAY DIFFRACTION99.65
1.74-1.810.24751420.20644454X-RAY DIFFRACTION99.63
1.81-1.890.23711410.19564451X-RAY DIFFRACTION99.5
1.89-1.990.23951440.19414499X-RAY DIFFRACTION99.85
1.99-2.120.21251410.1894454X-RAY DIFFRACTION99.72
2.12-2.280.20641430.1834489X-RAY DIFFRACTION99.59
2.28-2.510.21291440.18514519X-RAY DIFFRACTION99.76
2.51-2.870.20941450.19374566X-RAY DIFFRACTION99.94
2.87-3.620.21911450.18254570X-RAY DIFFRACTION99.49
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)
12.792808913190.363368587785-0.1753487095122.048340579020.6861611540222.29082126037-0.001833971678440.3201364503750.216365292949-0.1649467202550.0663049397452-0.0775876619234-0.1457009201480.0104113260721-0.06595807126660.108266725246-0.00615768465882-0.002315739786240.1098960163470.02785024267230.10681039451-20.14548772169.46765125752-12.4531259174
21.862350454610.1140658463-0.1688352329641.08520193038-0.5426616690192.435826301580.0598000770750.1049835184670.3763141386920.04221601973590.03021465784650.0959497956272-0.379557250427-0.13978154489-0.06851217991220.1440869587280.01737943480390.008855022147980.1112995650260.004753878216890.139120194921-29.35351164497.9828569975-7.03840018787
31.623797705860.2062883454990.1059685167870.6356685061860.6023604848343.073692548090.0102048896603-0.0784183134503-0.09583682618080.05526039864050.032153450107-0.04193278427850.128509383507-0.0165574681206-0.0474782252660.09651481297260.00871778587250.001504963535480.0687678428395-0.002568874478880.0670614041524-23.7961818682-5.599074425960.516282777317
42.306402180790.434349446364-0.03427205761932.21732861212-0.4254457949920.702266938740.024988152186-0.08146048975250.03725595856940.0734210102067-0.0230262255675-0.277082968977-0.02816512019730.108009784948-0.01232463403570.08403955207230.00250260749553-0.00537200042090.115251416629-0.02816388867060.109861764463-9.717351254941.34625281451-2.50631180262
53.702607708760.001142382244910.03492775544964.171406614871.652271511571.053951015460.0518924731370.1073324693630.319159537141-0.4756999764910.00680527331895-0.0407530135891-0.2898716104450.0166386907576-0.0659364929860.2594069584970.02434406173650.01890257389280.1617627561120.03190479555010.416614200942-37.0277600057-32.17263892120.957645108053
62.18179099037-1.379530694280.9546961926633.775194556080.3981704402792.420056994510.115911442593-0.00865769615822-0.244225668885-0.632640653714-0.09659159314570.5445772323770.2510475618520.0900053160607-0.04416447895260.3302135255830.0271222074171-0.04613477840970.2146950055210.0700255561180.509576791915-44.0559976145-32.3616541545-0.811790138329
70.651944682662-1.890810657591.090116190365.48922347178-3.196902332871.980902521560.4855056838440.597793883808-0.522868657513-0.735227660138-0.332458760037-0.7899779157170.1195683467390.303280371605-0.2200066237950.3404902300660.06131592179390.07672000390440.300969874039-0.05444156562810.575230417772-42.9612169431-13.3337123331.60375602211
81.67176295403-0.9482594688130.08377595129173.332260372621.351098310351.99638288059-0.232435950454-0.479871893021-0.3498630784970.4364840716260.331665756855-0.08724657621690.03442632577870.293283398748-0.08955368720760.335851297880.04095392779740.01902098731660.3903795019570.07024567606470.39098289461-35.8710624042-21.310084316313.2313161522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 34 )
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 85 )
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 142 )
4X-RAY DIFFRACTION4chain 'A' and (resid 143 through 206 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 39 )
6X-RAY DIFFRACTION6chain 'B' and (resid 40 through 73 )
7X-RAY DIFFRACTION7chain 'B' and (resid 74 through 85 )
8X-RAY DIFFRACTION8chain 'B' and (resid 86 through 206 )

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