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- PDB-9d40: Crystal structure of the catalytic region of human MASP-2 with sp... -

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Basic information

Entry
Database: PDB / ID: 9d40
TitleCrystal structure of the catalytic region of human MASP-2 with specific inhibitor Analog 20
ComponentsMannan-binding lectin serine protease 2 B chain
KeywordsHYDROLASE/INHIBITOR / Inhibitor / MASP2 / hydrolase / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


mannan-binding lectin-associated serine protease-2 / complement component C4b binding / Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / complement activation, lectin pathway / Initial triggering of complement / complement activation, classical pathway / calcium-dependent protein binding / peptidase activity / serine-type endopeptidase activity ...mannan-binding lectin-associated serine protease-2 / complement component C4b binding / Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / complement activation, lectin pathway / Initial triggering of complement / complement activation, classical pathway / calcium-dependent protein binding / peptidase activity / serine-type endopeptidase activity / calcium ion binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Peptidase S1A, complement C1r/C1S/mannan-binding / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / : / Calcium-binding EGF domain / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) ...Peptidase S1A, complement C1r/C1S/mannan-binding / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / : / Calcium-binding EGF domain / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
: / Mannan-binding lectin serine protease 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsSawyer, T.K. / Wibowo, A.S. / Carter, J. / Moussa, S.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Eur.J.Med.Chem. / Year: 2025
Title: Small molecule inhibitors of mannan-binding lectin-associated serine Proteases-2 and-3.
Authors: Nakhla, M.C. / Comita, J. / Shapiro, A.B. / Moussa, S.H. / Chen, A. / Eyermann, C.J. / O'Donnell, J.P. / Miller, A.A. / Granger, B.A.
History
DepositionAug 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mannan-binding lectin serine protease 2 B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0124
Polymers35,3661
Non-polymers6463
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.520, 40.980, 101.870
Angle α, β, γ (deg.)90.000, 97.820, 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-935-

HOH

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Components

#1: Protein Mannan-binding lectin serine protease 2 B chain


Mass: 35365.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MASP2 / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle(DE3) pLysS
References: UniProt: O00187, mannan-binding lectin-associated serine protease-2
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-A1A1Z / N-{[4-(2-amino-1H-imidazol-4-yl)phenyl]methyl}-2-[4-(benzenesulfonamido)phenyl]acetamide


Mass: 461.536 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H23N5O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.12 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.0 uL of protein (0.62 mg/mL MASP2) was mixed with 1.0 uL of reservoir solution (0.1 M Tris-HCl pH 7.8, 0.16 M NaCl, 31% (w/v) PEG 6000, 10% (v/v) glycerol, and 200 uM Analog 20) and ...Details: 1.0 uL of protein (0.62 mg/mL MASP2) was mixed with 1.0 uL of reservoir solution (0.1 M Tris-HCl pH 7.8, 0.16 M NaCl, 31% (w/v) PEG 6000, 10% (v/v) glycerol, and 200 uM Analog 20) and equilibrated against reservoir at 20 C. Crystals were cryoprotected in reservoir supplemented with 20% (v/v) glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95355 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95355 Å / Relative weight: 1
ReflectionResolution: 1.76→20.49 Å / Num. obs: 29662 / % possible obs: 99.71 % / Redundancy: 3.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.1087 / Net I/σ(I): 7.13
Reflection shellResolution: 1.76→1.823 Å / Rmerge(I) obs: 1.598 / Mean I/σ(I) obs: 0.89 / Num. unique obs: 11111 / CC1/2: 0.339

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Processing

Software
NameVersionClassification
xia2data reduction
xia2data scaling
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→20.49 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2538 1517 -
Rwork0.1979 28138 -
obs0.2005 29655 99.78 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→20.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2388 0 45 141 2574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.820.35381820.34372511X-RAY DIFFRACTION99.7
1.82-1.880.34051480.29882507X-RAY DIFFRACTION99.51
1.88-1.960.33061670.27182493X-RAY DIFFRACTION99.92
1.96-2.050.31091350.25342549X-RAY DIFFRACTION99.89
2.05-2.150.27241360.21822543X-RAY DIFFRACTION99.89
2.15-2.290.25521240.20662571X-RAY DIFFRACTION100
2.29-2.460.251360.20112559X-RAY DIFFRACTION99.93
2.46-2.710.23251240.19342543X-RAY DIFFRACTION99.74
2.71-3.10.25381420.19272573X-RAY DIFFRACTION99.74
3.1-3.910.2188910.16632620X-RAY DIFFRACTION99.63
3.91-20.490.22261320.17452669X-RAY DIFFRACTION99.72

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