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- PDB-9c16: Human biliverdin IX beta reductase in complex with NADP and BCT002029 -

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Basic information

Entry
Database: PDB / ID: 9c16
TitleHuman biliverdin IX beta reductase in complex with NADP and BCT002029
ComponentsFlavin reductase (NADPH)
KeywordsOXIDOREDUCTASE / NADP binding / heme degradation / thrombopoiesis
Function / homology
Function and homology information


FMN reductase (NADH) activity / biliverdin reductase [NAD(P)H] activity / flavin reductase (NADPH) / FMN reductase (NADPH) activity / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / megakaryocyte differentiation / riboflavin reductase (NADPH) activity / heme catabolic process / Heme degradation ...FMN reductase (NADH) activity / biliverdin reductase [NAD(P)H] activity / flavin reductase (NADPH) / FMN reductase (NADPH) activity / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / megakaryocyte differentiation / riboflavin reductase (NADPH) activity / heme catabolic process / Heme degradation / peptidyl-cysteine S-nitrosylase activity / negative regulation of insulin receptor signaling pathway / Cytoprotection by HMOX1 / intracellular membrane-bounded organelle / extracellular exosome / nucleoplasm / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / NAD(P)H-binding / NAD(P)-binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Flavin reductase (NADPH)
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsKreitler, D.F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL150927 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL153144 United States
CitationJournal: Nat Commun / Year: 2025
Title: Small molecule BLVRB redox inhibitor promotes megakaryocytopoiesis and stress thrombopoiesis in vivo.
Authors: Nesbitt, N.M. / Araldi, G.L. / Pennacchia, L. / Marchenko, N. / Assar, Z. / Muzzarelli, K.M. / Thekke Veedu, R.R. / Medel-Lacruz, B. / Lee, E. / Eisenmesser, E.Z. / Kreitler, D.F. / Bahou, W.F.
History
DepositionMay 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flavin reductase (NADPH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6543
Polymers22,5511
Non-polymers1,1032
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.091, 42.264, 66.148
Angle α, β, γ (deg.)90.000, 108.040, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-457-

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 / S-nitroso-CoA-assisted nitrosyltransferase / SNO-CoA-assisted nitrosyltransferase


Mass: 22550.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BLVRB, FLR, SCAN / Plasmid: pGEX / Details (production host): GST / Production host: Escherichia coli (E. coli)
References: UniProt: P30043, flavin reductase (NADPH), Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor, Transferases; Transferring nitrogenous groups; ...References: UniProt: P30043, 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
#2: Chemical ChemComp-A1ATI / (3M)-3-[(8R)-3-ethyl-7-oxo-2-phenyl-4,7-dihydropyrazolo[1,5-a]pyrimidin-5-yl]benzoic acid


Mass: 359.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H17N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.24 Å3/Da / Density % sol: 45.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 12% (w/v) PEG20000, 25% (v/v) MPD, 1 mM NADP+

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 2, 2024 / Details: KB bimorph
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.58→31.45 Å / Num. obs: 25464 / % possible obs: 92.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 16.94 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.08 / Rrim(I) all: 0.146 / Net I/σ(I): 5.7
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 2.7 % / Rmerge(I) obs: 1.393 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1287 / CC1/2: 0.329 / Rpim(I) all: 0.991 / Rrim(I) all: 1.722 / % possible all: 92.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→31.45 Å / SU ML: 0.2095 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.7201
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2261 1249 4.95 %
Rwork0.2063 23968 -
obs0.2073 25217 92.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.02 Å2
Refinement stepCycle: LAST / Resolution: 1.58→31.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1529 0 75 146 1750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01051667
X-RAY DIFFRACTIONf_angle_d1.13962290
X-RAY DIFFRACTIONf_chiral_restr0.0639267
X-RAY DIFFRACTIONf_plane_restr0.0098288
X-RAY DIFFRACTIONf_dihedral_angle_d17.6412594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.650.35821310.34182534X-RAY DIFFRACTION88.51
1.65-1.720.31661520.30472710X-RAY DIFFRACTION94.39
1.72-1.810.32431350.28922757X-RAY DIFFRACTION94.91
1.81-1.930.35521390.24742703X-RAY DIFFRACTION95.02
1.93-2.080.24181300.22362704X-RAY DIFFRACTION92.92
2.08-2.280.25071350.20642684X-RAY DIFFRACTION92.94
2.28-2.610.21381490.1932657X-RAY DIFFRACTION92.42
2.61-3.290.2051570.18432615X-RAY DIFFRACTION90.44
3.29-31.450.15821210.16672604X-RAY DIFFRACTION86.87

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