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- PDB-10ku: Structure of hNSP4-S218A bound to MCP3 at 2.09 A resolution -

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Basic information

Entry
Database: PDB / ID: 10ku
TitleStructure of hNSP4-S218A bound to MCP3 at 2.09 A resolution
Components
  • MCP3
  • Serine protease 57
KeywordsHYDROLASE / NSP4 / PROTEASE / MCP
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / protein maturation / azurophil granule lumen / heparin binding / serine-type endopeptidase activity / proteolysis / :
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / 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
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsTang, W. / Martinez, O.E. / Ultsch, M.H. / Sudhamsu, J.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche LTD Switzerland
CitationJournal: J.Mol.Biol. / Year: 2026
Title: Novel macrocyclic peptides as potent and selective inhibitors of human neutrophil serine protease 4.
Authors: Tang, W. / Ultsch, M. / Adaligil, E. / Tombling, B. / Fleming, S. / Wei, Y. / Martinez, O.E. / Song, A. / Lello, P.D. / Sudhamsu, J. / Cunningham, C.N. / Kirchhofer, D.
History
DepositionJan 25, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine protease 57
B: Serine protease 57
C: Serine protease 57
D: Serine protease 57
G: MCP3
I: MCP3
F: MCP3
E: MCP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,82132
Polymers107,5168
Non-polymers2,30624
Water6,161342
1
A: Serine protease 57
F: MCP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,64710
Polymers26,8792
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-86 kcal/mol
Surface area11130 Å2
MethodPISA
2
B: Serine protease 57
E: MCP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5519
Polymers26,8792
Non-polymers6727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-88 kcal/mol
Surface area11120 Å2
MethodPISA
3
C: Serine protease 57
G: MCP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2636
Polymers26,8792
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-55 kcal/mol
Surface area10900 Å2
MethodPISA
4
D: Serine protease 57
I: MCP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3597
Polymers26,8792
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-78 kcal/mol
Surface area10840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.041, 43.669, 124.030
Angle α, β, γ (deg.)90.00, 92.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Serine protease 57 / Neutrophil serine protease 4 / NSP4 / Serine protease 1-like protein 1


Mass: 25274.014 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRSS57, PRSSL1, UNQ782/PRO1599 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q6UWY2, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide
MCP3


Mass: 1604.946 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 25% (w/v) PEG 3350, 0.1 M Bis-Tris pH 5.5, 0.2 M LiSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 2.0.1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.09→123.9 Å / Num. obs: 54559 / % possible obs: 77.21 % / Redundancy: 4.4 % / CC1/2: 0.985 / Net I/σ(I): 5.8
Reflection shellResolution: 2.09→2.165 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2728 / CC1/2: 0.434

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Processing

Software
NameVersionClassification
PHENIX(1.20.1-4487_final: ???)refinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→123.9 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2622 2752 5.04 %
Rwork0.2282 --
obs0.2299 54552 77.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→123.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7489 0 122 342 7953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057976
X-RAY DIFFRACTIONf_angle_d0.79810874
X-RAY DIFFRACTIONf_dihedral_angle_d11.142824
X-RAY DIFFRACTIONf_chiral_restr0.0841204
X-RAY DIFFRACTIONf_plane_restr0.0061376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.130.3607130.3254213X-RAY DIFFRACTION7
2.13-2.170.2669220.2945513X-RAY DIFFRACTION15
2.17-2.210.3183410.2545743X-RAY DIFFRACTION23
2.21-2.230.3452270.2639427X-RAY DIFFRACTION31
2.26-2.30.3714940.28171670X-RAY DIFFRACTION57
2.3-2.350.29031520.27212515X-RAY DIFFRACTION77
2.35-2.410.29211520.2742890X-RAY DIFFRACTION86
2.41-2.480.34131550.28232955X-RAY DIFFRACTION90
2.48-2.550.30411770.2883146X-RAY DIFFRACTION94
2.55-2.630.38091570.283164X-RAY DIFFRACTION95
2.63-2.730.35421840.25823275X-RAY DIFFRACTION98
2.73-2.840.30231990.26393226X-RAY DIFFRACTION98
2.84-2.970.28871600.25153310X-RAY DIFFRACTION98
2.97-3.120.29222080.25323323X-RAY DIFFRACTION99
3.12-3.320.27281620.23653300X-RAY DIFFRACTION99
3.32-3.570.20211860.20823355X-RAY DIFFRACTION100
3.58-3.930.23951560.18883409X-RAY DIFFRACTION100
3.94-4.50.19461540.17563407X-RAY DIFFRACTION100
4.5-5.670.21581700.18563417X-RAY DIFFRACTION100
5.68-123.90.21771830.22313542X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.83120.10420.38371.07430.10291.37530.0721-0.00270.0130.026-0.0851-0.0066-0.0388-0.0328-0.00770.1403-0.00160.0010.0933-0.01130.063340.9306-25.085150.1405
22.23830.1845-0.16981.14460.18991.08770.0918-0.1044-0.01970.0565-0.08140.07380.0163-0.0268-0.01380.1437-0.00040.01330.0783-0.01260.068943.6652-4.726111.8886
32.0291-0.00890.40822.0946-0.50861.22910.08260.0833-0.01960.14620.04740.58580.0285-0.0191-0.09770.1240.0040.04160.1366-0.02910.345710.7559-0.367956.6355
41.61620.1038-0.50461.7603-0.15651.58380.0852-0.0090.0665-0.0960.0770.5202-0.1296-0.0736-0.10760.1182-0.0075-0.03550.1265-0.02780.357413.7014-29.14565.2893
52.30171.30830.68632.20220.19341.29050.204-0.1528-0.0260.0593-0.25230.14070.00540.2924-0.04840.13230.0290.01930.2443-0.020.278125.7851-1.595257.6224
62.4366-0.476-0.90631.83630.03961.5805-0.0430.09650.1418-0.1826-0.2251-0.17050.14990.03660.08370.2387-0.0284-0.03590.21720.02510.3428.5463-28.13894.2952
73.97640.2045-0.03751.28610.00632.2717-0.00810.025-0.0820.1115-0.18470.04080.34050.2040.03770.20040.00610.0050.054-0.00480.120231.7673-35.151744.0794
82.0373-0.20580.66440.61210.79831.4821-0.2126-0.23940.15370.03410.02490.1057-0.3229-0.0333-0.1080.16310.01630.01090.06220.02270.272834.46615.527517.6996
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 302 )
2X-RAY DIFFRACTION2chain 'B' and (resid 16 through 302 )
3X-RAY DIFFRACTION3chain 'C' and (resid 16 through 302 )
4X-RAY DIFFRACTION4chain 'D' and (resid 16 through 302 )
5X-RAY DIFFRACTION5chain 'G' and (resid 1 through 13 )
6X-RAY DIFFRACTION6chain 'I' and (resid 1 through 13 )
7X-RAY DIFFRACTION7chain 'F' and (resid 1 through 13 )
8X-RAY DIFFRACTION8chain 'E' and (resid 1 through 13 )

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