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- PDB-9d3y: Crystal structure of the catalytic region of human MASP-2 with sp... -

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Basic information

Entry
Database: PDB / ID: 9d3y
TitleCrystal structure of the catalytic region of human MASP-2 with specific inhibitor Compound S2
ComponentsMannan-binding lectin serine protease 2 B chain
KeywordsHYDROLASE / Inhibitor / MASP2
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: 2.08 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)36,3658
Polymers35,3661
Non-polymers9997
Water1,20767
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)72.770, 41.050, 102.920
Angle α, β, γ (deg.)90.000, 98.010, 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 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.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-A1A1Y / (2S)-N-[2-(2-amino-1H-1,3-benzimidazol-5-yl)ethyl]-1-[(2R,4S)-4-phenylpiperidine-2-carbonyl]azetidine-2-carboxamide


Mass: 446.545 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H30N6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
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 Compound S2) 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 Compound S2) 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: 2.08→35.67 Å / Num. obs: 18318 / % possible obs: 99.55 % / Redundancy: 3.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.1555 / Net I/σ(I): 6.44
Reflection shellResolution: 2.08→2.154 Å / Rmerge(I) obs: 1.545 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1815 / CC1/2: 0.348

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Processing

Software
NameVersionClassification
xia2data reduction
xia2data scaling
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→35.67 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.261 951 -
Rwork0.2066 17361 -
obs-18312 99.57 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.08→35.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2429 0 69 67 2565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.190.35681370.3122457X-RAY DIFFRACTION99.5
2.19-2.330.30131620.26832423X-RAY DIFFRACTION99.61
2.33-2.510.27941170.24542453X-RAY DIFFRACTION99.5
2.51-2.760.28871190.23342513X-RAY DIFFRACTION99.51
2.76-3.160.27411540.21142456X-RAY DIFFRACTION99.73
3.16-3.980.22171280.1782479X-RAY DIFFRACTION99.43
3.98-35.670.24671340.17972580X-RAY DIFFRACTION99.71

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