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- PDB-2plx: Trypsin complexed to a synthetic peptide from Veronica hederifolia -

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Basic information

Entry
Database: PDB / ID: 2plx
TitleTrypsin complexed to a synthetic peptide from Veronica hederifolia
Components
  • Cationic trypsin
  • Peptide Inhibitor
KeywordsHYDROLASE / Helix-turn-helix
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / 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
CITRATE ANION / Serine protease 1 / Trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsConners, R. / Brady, R.L.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: An Unusual Helix-Turn-Helix Protease Inhibitory Motif in a Novel Trypsin Inhibitor from Seeds of Veronica (Veronica hederifolia L.)
Authors: Conners, R. / Konarev, A.V. / Forsyth, J. / Lovegrove, A. / Marsh, J. / Joseph-Horne, T. / Shewry, P. / Brady, R.L.
History
DepositionApr 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cationic trypsin
B: Peptide Inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8556
Polymers26,4422
Non-polymers4134
Water5,729318
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.558, 41.521, 51.189
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a heterodimer of chain A and chain B and is identical to the asymmetric unit.

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Cationic trypsin


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Pancreas / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin
#2: Protein/peptide Peptide Inhibitor


Mass: 3117.672 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Chemicall synthesized. Occurs naturally in Veronica hederifolia.
References: UniProt: P85981*PLUS

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Non-polymers , 4 types, 322 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.3-1.5M Na Citrate, 0.1M Na Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 23, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.56→56.8 Å / Num. all: 28405 / Num. obs: 28405 / % possible obs: 80.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.044 / Χ2: 1.075 / Net I/σ(I): 20.7
Reflection shellResolution: 1.56→1.62 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.611 / Num. unique all: 397 / Χ2: 0.886 / % possible all: 11.5

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å33.52 Å
Translation2.5 Å33.52 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SFI

1sfi


Resolution: 1.56→56.8 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.197 / WRfactor Rwork: 0.147 / SU B: 3.077 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.188 1442 5.1 %RANDOM
Rwork0.143 ---
all0.145 28405 --
obs0.145 28371 80.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.031 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2---0.34 Å20 Å2
3---0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.56→56.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1842 0 26 318 2186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221990
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.9592720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7335278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.3325.61673
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.63615334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.485155
X-RAY DIFFRACTIONr_chiral_restr0.1390.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021498
X-RAY DIFFRACTIONr_nbd_refined0.2170.2926
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21390
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2275
X-RAY DIFFRACTIONr_metal_ion_refined0.0690.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.247
X-RAY DIFFRACTIONr_mcbond_it0.9111.51311
X-RAY DIFFRACTIONr_mcangle_it1.32522082
X-RAY DIFFRACTIONr_scbond_it2.163774
X-RAY DIFFRACTIONr_scangle_it2.8454.5625
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree: 0.011 / Total num. of bins used: 20

Resolution (Å)Num. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.56-1.601100.63619626017.92
1.601-1.645370.39683247929.044
1.645-1.692590.2651108240748.484
1.692-1.744810.1711464238164.889
1.744-1.8021080.1611758230181.095
1.802-1.865920.1621997220294.868
1.865-1.9351020.152027216798.246
1.935-2.014940.1411949207698.41
2.014-2.103950.1361863198198.839
2.103-2.206850.1351821192099.271
2.206-2.3251020.1311715182999.344
2.325-2.466960.1351608171599.359
2.466-2.636790.1351565164899.757
2.636-2.846820.14414241506100
2.846-3.117710.1331338141099.929
3.117-3.484710.11812241295100
3.484-4.02630.1091066113099.912
4.02-4.918450.10693397999.898
4.918-6.929470.173745792100
6.929-56.796230.24844547897.908
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)
10.01570.04980.09150.64710.06170.64010.0068-0.04870.020.098-0.0062-0.04330.0743-0.076-0.0006-0.05310.0020.0066-0.0560.0026-0.107920.107914.56523.8084
24.7461-2.3028-0.58284.0735-0.00052.25310.0550.08920.2026-0.0327-0.073-0.2026-0.18620.17130.018-0.036-0.0136-0.0088-0.08690.0066-0.140626.830521.70915.9913
33.9377-0.0382.09740.1845-0.54062.5875-0.04570.08240.23070.1414-0.06630.0062-0.32820.10760.112-0.0401-0.0211-0.0013-0.08340.0098-0.104926.122424.242910.6499
40.04080.3143-0.09443.8682.90359.3403-0.1603-0.18540.1103-0.14570.07670.14-0.16190.05520.0836-0.05870.0014-0.0203-0.0902-0.0073-0.092424.929323.588327.5233
50.2860.49940.61380.8961.738819.8360.13210.01880.0431-0.05960.0729-0.0156-0.12560.4292-0.2049-0.0680.0255-0.0108-0.05090.0021-0.06531.995823.578119.6722
67.13160.50882.22381.082-0.32261.9757-0.10380.24110.2182-0.14390.0309-0.0177-0.12140.00410.0729-0.0420.00510.0175-0.0810.0023-0.115221.739420.76651.4433
77.63122.925-12.68443.0851-8.60828.2291-0.1271-0.3641-0.0056-0.1658-0.317-0.39870.9760.91190.44410.0034-0.0079-0.0341-0.0329-0.0235-0.078236.515718.391420.5335
83.40071.9126-0.06171.87720.75670.7825-0.07410.0223-0.1831-0.03340.1072-0.0380.01730.032-0.0332-0.04130.0228-0.0089-0.08290.021-0.101824.31775.022111.6684
94.70246.32054.981822.842214.90429.9739-0.0060.0968-0.19940.38640.01540.33990.3290.0697-0.0095-0.06940.00390.0128-0.0862-0.0086-0.105715.10387.61917.5637
1020.0317-2.432-7.84727.24470.35168.52590.5320.7690.13130.1404-0.25480.3566-0.424-0.9057-0.27730.00030.05010.0015-0.05630.0018-0.143310.482121.67422.5134
1115.0716-9.18368.13778.9143-5.865112.3167-0.2825-0.25560.41910.24030.03360.2559-0.941-0.82230.24890.02810.05580.0077-0.0016-0.0391-0.072111.775123.86924.8413
124.6567.26018.850912.127812.300519.61540.1377-0.2134-0.26890.3293-0.11010.02690.2172-0.1981-0.0276-0.08720.02450.0108-0.0922-0.0029-0.087812.21828.778319.304
131.5954-4.06332.332916.472-4.65833.68030.22570.3956-0.3057-0.50570.0310.16440.4263-0.0321-0.2567-0.01550.0059-0.0045-0.0055-0.0197-0.08584.82057.98323.4885
142.51930.67810.84981.2812-1.59543.3153-0.09410.15010.0242-0.13460.07490.0822-0.0529-0.09940.0192-0.0546-0.00010.002-0.0533-0.0032-0.108910.324611.95132.3006
159.04093.43113.38435.74564.98034.341-0.1142-0.4047-0.1357-0.00840.00720.5225-0.01820.25430.107-0.0377-0.02160.0271-0.03880.0497-0.07091.94639.073616.7829
162.3884-0.0862-0.07360.3351-0.6541.30120.047-0.0333-0.1126-0.083-0.0460.06720.074-0.0159-0.001-0.080.0009-0.0068-0.09750.0046-0.115316.088713.892915.3535
174.0752-2.50622.36324.1124-0.86871.9414-0.06890.01030.058-0.02050.0568-0.03640.14590.01990.0121-0.06490.00720.0129-0.11620.0043-0.144816.071513.32999.4952
187.48576.45880.811512.17674.38139.14960.15830.02820.00490.2567-0.3140.16620.2108-0.36670.1557-0.11610.02110.005-0.09020.0084-0.07050.4416.011813.4057
197.9004-1.3812-3.03211.36630.93291.41570.14650.2002-0.2526-0.1388-0.13790.03430.016-0.1153-0.0087-0.05240.0053-0.0058-0.08620.007-0.13217.157811.21325.2455
2023.27225.80170.48865.8873-1.19172.4476-0.05590.17130.152-0.02880.1285-0.0563-0.04750.3626-0.0726-0.04210.01540.0203-0.05780.0056-0.108534.085914.53022.4154
2115.3495-4.22910.31589.0627-7.447718.7735-0.2070.6367-0.2309-0.73260.1180.29150.5714-0.59770.089-0.052-0.0084-0.0032-0.0516-0.0036-0.06296.381427.46792.3178
220.8554-0.03090.49491.5151-1.1361.1120.0073-0.06210.03350.1716-0.02580.1286-0.0979-0.09210.0185-0.0486-0.00060.0245-0.0936-0.014-0.092511.77726.90111.376
232.7597-0.3654-1.34957.4985-6.94577.51190.1503-0.02940.36070.1818-0.0632-0.1127-0.1412-0.0072-0.087-0.0299-0.0090.0209-0.1229-0.0192-0.081413.597834.5688.1734
2416.67694.73483.573421.220212.407916.9938-0.15390.86610.835-1.4950.77750.5736-1.13130.0884-0.62370.0833-0.05520.0092-0.0040.067-0.021910.693437.1178-0.4354
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 33
2X-RAY DIFFRACTION2A34 - 50
3X-RAY DIFFRACTION3A51 - 65
4X-RAY DIFFRACTION4A66 - 76
5X-RAY DIFFRACTION5A77 - 89
6X-RAY DIFFRACTION6A90 - 107
7X-RAY DIFFRACTION7A108 - 117
8X-RAY DIFFRACTION8A118 - 133
9X-RAY DIFFRACTION9A134 - 140
10X-RAY DIFFRACTION10A141 - 146
11X-RAY DIFFRACTION11A147 - 155
12X-RAY DIFFRACTION12A156 - 162
13X-RAY DIFFRACTION13A163 - 172
14X-RAY DIFFRACTION14A173 - 184
15X-RAY DIFFRACTION15A185 - 188
16X-RAY DIFFRACTION16A189 - 203
17X-RAY DIFFRACTION17A209 - 217
18X-RAY DIFFRACTION18A219 - 223
19X-RAY DIFFRACTION19A224 - 236
20X-RAY DIFFRACTION20A237 - 245
21X-RAY DIFFRACTION21B6 - 11
22X-RAY DIFFRACTION22B12 - 19
23X-RAY DIFFRACTION23B20 - 26
24X-RAY DIFFRACTION24B27 - 31

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