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- PDB-13dz: X-ray crystal structure of human biliverdin beta IX reductase in ... -

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Basic information

Entry
Database: PDB / ID: 13dz
TitleX-ray crystal structure of human biliverdin beta IX reductase in complex with NADP and BCT002104
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 / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / riboflavin reductase (NADPH) activity / megakaryocyte differentiation / heme catabolic process / Heme degradation ...FMN reductase (NADH) activity / biliverdin reductase [NAD(P)H] activity / flavin reductase (NADPH) / FMN reductase (NADPH) activity / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / riboflavin reductase (NADPH) activity / megakaryocyte differentiation / heme catabolic process / Heme degradation / peptidyl-cysteine S-nitrosylase activity / negative regulation of insulin receptor signaling pathway / Cytoprotection by HMOX1 / extracellular exosome / cytosol / cytoplasm
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: 1.72 Å
AuthorsKreitler, D.F.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL153144 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL150927 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM133893 United States
CitationJournal: J.Med.Chem. / Year: 2026
Title: A Structure-guided Active Site Affinity Ligand Unmasks a Stress-Sensitizing Role for BLVRB in the Endoplasmic Reticulum.
Authors: Thekke Veedu, R.R. / Sheriff, J. / Nesbitt, N.M. / Marchenko, N. / Pennacchia, L. / Ginex, T. / Hearing, P. / Kreitler, D.F. / Bahou, W.F.
History
DepositionMay 1, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2026Provider: 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)23,9244
Polymers22,5511
Non-polymers1,3733
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.156, 42.385, 66.738
Angle α, β, γ (deg.)90.000, 107.410, 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

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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-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
#3: Chemical ChemComp-A1DFI / (3M)-3-[(2M,8S)-3-ethyl-2-(3-{[(3-methoxyphenyl)carbamamido]methyl}phenyl)-7-oxo-4,7-dihydropyrazolo[1,5-a]pyrimidin-5-yl]benzoic acid


Mass: 537.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H27N5O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: protein solution: BLVRB at 18 mg/mL in 50 mM Bis-Tris, pH 6.5, 50 mM NaCl, 1 mM DTT, 1 mM NADP+ well solution: 0.1 M MES monohydrate pH 6.5, 10-12% (w/v) PEG 20,000, and 25% (v/v) MPD. ...Details: protein solution: BLVRB at 18 mg/mL in 50 mM Bis-Tris, pH 6.5, 50 mM NaCl, 1 mM DTT, 1 mM NADP+ well solution: 0.1 M MES monohydrate pH 6.5, 10-12% (w/v) PEG 20,000, and 25% (v/v) MPD. Crystallization droplets comprised 0.5 uL protein solution was mixed with 0.5 uL of well solution. BLVRB/NADP+ crystals were soaked for approximately 1 hour in a drop containing 2.5-5 mM BCT2104 (dissolved in 100% DMSO) and vitrified with 30% (v/v) glycerol as cryoprotectant.

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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: May 25, 2024 / Details: KB bimorph mirrors
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: 1.72→31.841 Å / Num. obs: 21585 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 21.64 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.078 / Rrim(I) all: 0.152 / Net I/σ(I): 6.1
Reflection shellResolution: 1.725→1.754 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.492 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1091 / CC1/2: 0.343 / Rpim(I) all: 0.948 / Rrim(I) all: 1.774 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
PHASERphasing
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→31.84 Å / SU ML: 0.2522 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.6835
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2207 1123 5.23 %
Rwork0.1948 20339 -
obs0.1962 21462 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.12 Å2
Refinement stepCycle: LAST / Resolution: 1.72→31.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1529 0 94 151 1774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00641686
X-RAY DIFFRACTIONf_angle_d1.08252314
X-RAY DIFFRACTIONf_chiral_restr0.0547267
X-RAY DIFFRACTIONf_plane_restr0.0074290
X-RAY DIFFRACTIONf_dihedral_angle_d13.6576620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.80.40191300.35612444X-RAY DIFFRACTION95.72
1.8-1.90.38761230.30492568X-RAY DIFFRACTION99.74
1.9-2.020.27381190.25912544X-RAY DIFFRACTION99.85
2.02-2.170.24371690.21022519X-RAY DIFFRACTION99.7
2.17-2.390.24461430.1862546X-RAY DIFFRACTION99.67
2.39-2.740.25231430.17982546X-RAY DIFFRACTION99.81
2.74-3.450.19541560.17362525X-RAY DIFFRACTION99.33
3.45-31.840.16521400.16392647X-RAY DIFFRACTION99.75

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