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- PDB-4q80: Neutrophil serine protease 4 (PRSS57) with val-leu-lys-chlorometh... -

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Basic information

Entry
Database: PDB / ID: 4q80
TitleNeutrophil serine protease 4 (PRSS57) with val-leu-lys-chloromethylketone (VLK-cmk)
ComponentsSerine protease 57
KeywordsHYDROLASE/HYDROLASE INHIBITOR / trypsin homology / peptidase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / azurophil granule lumen / heparin binding / serine-type endopeptidase activity / proteolysis / extracellular space
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold ...Serine proteases, trypsin family, histidine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
D-VAL-LEU-LYS-chloromethylketone / Chem-2YS / Serine protease 57
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.07 Å
AuthorsEigenbrot, C. / Lin, S.J. / Dong, K.C.
CitationJournal: Structure / Year: 2014
Title: Structures of neutrophil serine protease 4 reveal an unusual mechanism of substrate recognition by a trypsin-fold protease.
Authors: Lin, S.J. / Dong, K.C. / Eigenbrot, C. / van Lookeren Campagne, M. / Kirchhofer, D.
History
DepositionApr 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_molecule.asym_id / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2868
Polymers54,0062
Non-polymers2,2806
Water0
1
A: Serine protease 57
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0414
Polymers27,0031
Non-polymers1,0393
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine protease 57
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2454
Polymers27,0031
Non-polymers1,2423
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.707, 89.707, 108.628
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Serine protease 57 / / Serine protease 1-like protein 1


Mass: 27002.900 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRSS57, PRSSL1, UNQ782/PRO1599 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q6UWY2, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-2YS / D-valyl-N-[(2S,3S)-7-amino-1-chloro-2-hydroxyheptan-3-yl]-L-leucinamide / D-VAL-LEU-LYS-chloromethylketone


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 392.964 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H37ClN4O3 / References: D-VAL-LEU-LYS-chloromethylketone
Sequence detailsNATURAL VARIANT DESCRIBED IN THE UNIPROT ENTRY Q6UWY2

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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: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG-3350, 0.2 M potassium acetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 5, 2011
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 3.07→50 Å / Num. all: 9241 / Num. obs: 9240 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 80.67 Å2 / Rsym value: 0.154 / Net I/σ(I): 12.5

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Processing

Software
NameVersionClassification
BOSdata collection
BUSTER2.11.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HNE

1hne


Resolution: 3.07→44.85 Å / Cor.coef. Fo:Fc: 0.9241 / Cor.coef. Fo:Fc free: 0.8774 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2402 423 4.58 %RANDOM
Rwork0.1852 ---
all0.19 9241 --
obs0.1877 9240 99.1 %-
Displacement parametersBiso mean: 62.37 Å2
Baniso -1Baniso -2Baniso -3
1--3.6189 Å20 Å20 Å2
2---3.6189 Å20 Å2
3---7.2379 Å2
Refine analyzeLuzzati coordinate error obs: 0.538 Å
Refinement stepCycle: LAST / Resolution: 3.07→44.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3562 0 148 0 3710
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093829HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.235220HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1289SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes50HARMONIC2
X-RAY DIFFRACTIONt_gen_planes587HARMONIC5
X-RAY DIFFRACTIONt_it3829HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.77
X-RAY DIFFRACTIONt_other_torsion18.26
X-RAY DIFFRACTIONt_chiral_improper_torsion495SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4219SEMIHARMONIC4
LS refinement shellResolution: 3.07→3.43 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3422 108 4.16 %
Rwork0.2109 2487 -
all0.2161 2595 -
obs--99.1 %
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)
15.75571.5646-1.37094.1848-0.08542.47420.10.37530.1349-0.4366-0.18410.3895-0.294-0.37050.0841-0.07850.10850.0446-0.0057-0.0126-0.0924-7.4685-29.518-7.5481
20.30041.60112.14664.8455-0.52812.08680.06340.23120.0985-0.50740.0308-0.0281-0.3557-0.0598-0.09420.03540.08170.1068-0.05260.0722-0.16071.0786-23.9561-7.5431
30.9013-0.96991.39982.80863.0812.648-0.01330.03710.12820.0569-0.0396-0.0383-0.0746-0.02780.05290.1034-0.07370.1052-0.054-0.1109-0.0711.6373-24.804311.4635
42.9257-0.8817-0.34645.53972.26482.11680.2824-0.31290.25590.2452-0.1744-0.22840.1439-0.2269-0.108-0.1246-0.09070.0603-0.014-0.0584-0.14931.8895-34.22124.4832
56.56151.3924-0.43992.73022.77683.1346-0.02080.14840.0843-0.19850.0685-0.43920.030.3897-0.0477-0.1408-0.00360.1012-0.10040.03170.030324.8141-52.8506-17.9498
61.47-0.6672-0.56724.05141.5033.96640.05540.20570.1116-0.2812-0.1431-0.25360.0494-0.20850.0877-0.1306-0.00170.0924-0.00820.0113-0.087516.8999-55.8228-23.6346
7-1.5070.04-3.18264.38231.18290.2474-0.02180.1005-0.0535-0.00650.0103-0.00370.02090.01220.01150.1581-0.0550.0555-0.1001-0.0640.171913.4077-70.1867-11.9429
83.8005-1.1238-2.0032.52981.85184.6444-0.06-0.129-0.48330.3482-0.1282-0.22860.725-0.16730.1882-0.0628-0.0852-0.0223-0.22770.0507-0.007513.9176-59.5621-8.4904
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|16 - A|67 }A16 - 67
2X-RAY DIFFRACTION2{ A|68 - A|110 }A68 - 110
3X-RAY DIFFRACTION3{ A|111 - A|128 }A111 - 128
4X-RAY DIFFRACTION4{ A|129 - A|233 }A129 - 233
5X-RAY DIFFRACTION5{ B|16 - B|67 }B16 - 67
6X-RAY DIFFRACTION6{ B|68 - B|110 }B68 - 110
7X-RAY DIFFRACTION7{ B|111 - B|128 }B111 - 128
8X-RAY DIFFRACTION8{ B|129 - B|233 }B129 - 233

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