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- PDB-9iud: High resolution structure of Lectin-Like ox-LDL Receptor 1 with B... -

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Basic information

Entry
Database: PDB / ID: 9iud
TitleHigh resolution structure of Lectin-Like ox-LDL Receptor 1 with BI-0115 in space group P 21 21 21
ComponentsOxidized low-density lipoprotein receptor 1
KeywordsLIPID BINDING PROTEIN / inhibitor / complex
Function / homology
Function and homology information


low-density lipoprotein particle receptor activity / lipoprotein metabolic process / blood circulation / leukocyte cell-cell adhesion / tertiary granule membrane / immune system process / specific granule membrane / Cell surface interactions at the vascular wall / carbohydrate binding / receptor complex ...low-density lipoprotein particle receptor activity / lipoprotein metabolic process / blood circulation / leukocyte cell-cell adhesion / tertiary granule membrane / immune system process / specific granule membrane / Cell surface interactions at the vascular wall / carbohydrate binding / receptor complex / membrane raft / inflammatory response / intracellular membrane-bounded organelle / Neutrophil degranulation / proteolysis / extracellular region / nucleoplasm / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / Natural killer cell receptor-like, C-type lectin-like domain / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
Chem-NJT / Oxidized low-density lipoprotein receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsKhan, M.A. / Arulandu, A.
Funding support India, 1items
OrganizationGrant numberCountry
Indian Council of Medical ResearchNCD/Adhoc/216/2021-2022 India
CitationJournal: To Be Published
Title: High resolution structure of Lectin-Like ox-LDL Receptor 1 with BI-0115 in space group P 21 21 21
Authors: khan, M.A. / Arulandu, A.
History
DepositionJul 20, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxidized low-density lipoprotein receptor 1
B: Oxidized low-density lipoprotein receptor 1
C: Oxidized low-density lipoprotein receptor 1
D: Oxidized low-density lipoprotein receptor 1
E: Oxidized low-density lipoprotein receptor 1
F: Oxidized low-density lipoprotein receptor 1
G: Oxidized low-density lipoprotein receptor 1
H: Oxidized low-density lipoprotein receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,33021
Polymers125,3508
Non-polymers1,98013
Water12,592699
1
A: Oxidized low-density lipoprotein receptor 1
B: Oxidized low-density lipoprotein receptor 1
C: Oxidized low-density lipoprotein receptor 1
D: Oxidized low-density lipoprotein receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,80312
Polymers62,6754
Non-polymers1,1288
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8130 Å2
ΔGint-29 kcal/mol
Surface area23350 Å2
MethodPISA
2
E: Oxidized low-density lipoprotein receptor 1
F: Oxidized low-density lipoprotein receptor 1
G: Oxidized low-density lipoprotein receptor 1
H: Oxidized low-density lipoprotein receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5279
Polymers62,6754
Non-polymers8525
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-23 kcal/mol
Surface area23730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.545, 110.246, 117.057
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Oxidized low-density lipoprotein receptor 1 / Ox-LDL receptor 1 / C-type lectin domain family 8 member A / Lectin-like oxidized LDL receptor 1 / ...Ox-LDL receptor 1 / C-type lectin domain family 8 member A / Lectin-like oxidized LDL receptor 1 / LOX-1 / Lectin-like oxLDL receptor 1 / hLOX-1 / Lectin-type oxidized LDL receptor 1


Mass: 15668.785 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OLR1, CLEC8A, LOX1 / Production host: Escherichia coli B (bacteria) / References: UniProt: P78380
#2: Chemical
ChemComp-NJT / 9-chloranyl-5-propyl-11~{H}-pyrido[2,3-b][1,4]benzodiazepin-6-one


Mass: 287.744 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H14ClN3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 699 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium formate dihydrate, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→80.25 Å / Num. obs: 71550 / % possible obs: 94.9 % / Redundancy: 9.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.041 / Rrim(I) all: 0.128 / Net I/σ(I): 11.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.97-2.018.10.99637480.8030.3721.064100
5.364-80.250.05640290.9960.0190.0699.9

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Processing

Software
NameVersionClassification
PHENIX(1.18.2-3874)refinement
PHENIX(1.18.2-3874)model building
PHASER2.8.3phasing
autoPROC1.0.5data processing
autoPROCdata reduction
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→41.27 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2414 3691 5.17 %
Rwork0.2026 --
obs0.2047 71432 94.71 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33 Å2
Refinement stepCycle: LAST / Resolution: 1.98→41.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8448 0 134 699 9281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098859
X-RAY DIFFRACTIONf_angle_d1.37412026
X-RAY DIFFRACTIONf_dihedral_angle_d22.7071240
X-RAY DIFFRACTIONf_chiral_restr0.061201
X-RAY DIFFRACTIONf_plane_restr0.0091589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-20.29031160.26082743X-RAY DIFFRACTION100
2-2.030.33961500.25482725X-RAY DIFFRACTION100
2.03-2.060.2821430.26142420X-RAY DIFFRACTION94
2.06-2.090.3595700.24741360X-RAY DIFFRACTION59
2.09-2.120.26891260.24332754X-RAY DIFFRACTION100
2.12-2.160.28531300.24322728X-RAY DIFFRACTION100
2.16-2.190.2621400.23792682X-RAY DIFFRACTION100
2.19-2.230.29741460.23752684X-RAY DIFFRACTION98
2.23-2.280.2685380.2365753X-RAY DIFFRACTION28
2.28-2.320.28821480.22722746X-RAY DIFFRACTION100
2.32-2.370.27621630.22872708X-RAY DIFFRACTION100
2.37-2.430.27591630.22572708X-RAY DIFFRACTION100
2.43-2.490.28551660.22512710X-RAY DIFFRACTION100
2.49-2.560.28651440.22722760X-RAY DIFFRACTION100
2.56-2.630.25421400.22782717X-RAY DIFFRACTION100
2.63-2.720.30651470.22082733X-RAY DIFFRACTION100
2.72-2.810.24031340.2182774X-RAY DIFFRACTION100
2.81-2.930.30751430.22392745X-RAY DIFFRACTION100
2.93-3.060.2841550.22552760X-RAY DIFFRACTION100
3.06-3.220.24191400.19622739X-RAY DIFFRACTION100
3.22-3.420.22591600.19422751X-RAY DIFFRACTION100
3.42-3.690.19111550.18372767X-RAY DIFFRACTION100
3.69-4.060.21411620.1742773X-RAY DIFFRACTION100
4.06-4.640.1931730.15762767X-RAY DIFFRACTION100
4.64-5.850.20821780.17412811X-RAY DIFFRACTION100
5.85-41.270.22451610.19342923X-RAY DIFFRACTION99

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