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- PDB-6t0m: Cationic Trypsin in Complex with a D-Phe-Pro-diaminopyridine deri... -

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Basic information

Entry
Database: PDB / ID: 6t0m
TitleCationic Trypsin in Complex with a D-Phe-Pro-diaminopyridine derivative
ComponentsCationic trypsin
KeywordsHYDROLASE / PROTEASE / SERINE PROTEASE / DIGESTION / METAL ION BINDING
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine 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 ...: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine 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
Chem-GOZ / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsNgo, K. / Heine, A. / Klebe, G.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Protein-Induced Change in Ligand Protonation during Trypsin and Thrombin Binding: Hint on Differences in Selectivity Determinants of Both Proteins?
Authors: Ngo, K. / Collins-Kautz, C. / Gerstenecker, S. / Wagner, B. / Heine, A. / Klebe, G.
History
DepositionOct 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4816
Polymers25,8061
Non-polymers6755
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-25 kcal/mol
Surface area8990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.454, 56.756, 66.691
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cationic trypsin


Mass: 25806.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00760, trypsin

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Non-polymers , 5 types, 176 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOZ / (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[[2,6-bis(azanyl)pyridin-4-yl]methyl]pyrrolidine-2-carboxamide


Mass: 382.459 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26N6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

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Details

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 Å3/Da / Density % sol: 38.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M (NH4)2SO4, 0.1 M imidazole, 0.1% (w/v) sodium azide, 25-27% (w/v) PEG8000
PH range: 7-8

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.507→43.223 Å / Num. obs: 33113 / % possible obs: 99.4 % / Redundancy: 5.75 % / Biso Wilson estimate: 15.96 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.06 / Rsym value: 0.055 / Net I/σ(I): 17.54
Reflection shellResolution: 1.51→1.6 Å / Mean I/σ(I) obs: 3.12 / Num. unique obs: 5172 / CC1/2: 0.858 / Rrim(I) all: 0.537 / Rsym value: 0.487

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MNK

5mnk


Resolution: 1.51→43.22 Å / SU ML: 0.1201 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.4187
RfactorNum. reflection% reflection
Rfree0.1709 1655 5 %
Rwork0.1482 --
obs0.1494 33111 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.5 Å2
Refinement stepCycle: LAST / Resolution: 1.51→43.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1610 0 42 171 1823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00731749
X-RAY DIFFRACTIONf_angle_d0.93492387
X-RAY DIFFRACTIONf_chiral_restr0.0647265
X-RAY DIFFRACTIONf_plane_restr0.0067324
X-RAY DIFFRACTIONf_dihedral_angle_d9.24531060
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.550.22721300.19452476X-RAY DIFFRACTION95.21
1.55-1.60.19691350.16942586X-RAY DIFFRACTION99.96
1.6-1.660.18861370.15132597X-RAY DIFFRACTION99.74
1.66-1.730.17861370.1422605X-RAY DIFFRACTION100
1.73-1.80.16711370.13692594X-RAY DIFFRACTION99.85
1.8-1.90.17241360.13322599X-RAY DIFFRACTION99.74
1.9-2.020.15641390.132623X-RAY DIFFRACTION99.78
2.02-2.170.14911370.12732612X-RAY DIFFRACTION100
2.17-2.390.151390.13092634X-RAY DIFFRACTION99.68
2.39-2.740.18771390.14482651X-RAY DIFFRACTION99.93
2.74-3.450.1671410.15182682X-RAY DIFFRACTION99.68
3.45-43.220.17391480.1642797X-RAY DIFFRACTION99.7
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)
10.2043029708650.006207357453340.02737490697850.2054332983540.07131275389220.2550230564430.00582637874208-0.0717621593684-0.05262400275230.120847617276-0.0170569520782-0.07605460494060.00371307519282-0.0193081323291-2.6673077433E-50.181229045656-0.013657444277-0.01132157051660.1565130353630.007247962774610.142937215702-2.47747374934-22.23078787620.3708987504
20.257681041037-0.243369757684-0.04154557920160.268750162705-0.03035962575560.120823370358-0.0240096530587-0.0763460438830.008386590523110.0505213512963-0.003588583667030.0236909734588-0.061330697874-0.0706634897673-3.094091674E-50.180990159293-0.0276294838536-0.0009739345805690.1571536595160.008139475059550.152394798399-9.7389832819-21.211391324413.4789199307
30.3209352080230.0342307588128-0.3021989034360.3571121326910.0764795460440.3676553544450.03666585456370.0781518018245-0.0261665362166-0.0483868832282-0.0194467181002-0.03068280787410.019042670768-0.01639736951913.47734625458E-50.124871023204-0.000300475338996-0.006232838854170.1414234981610.003418711495570.1438130919620.711448099332-21.80686782240.641628111824
40.3967745045450.09085084129430.1771919773610.317167056589-0.1816622824640.2498430253490.01076088025770.0839450351126-0.0850716830282-0.00857106013922-0.08011165894090.03411769921190.0571556552771-0.0584094526274-0.0001352546991230.140453299778-0.00638137442475-0.01241981311860.158128884865-0.009638160260820.142884152576-8.56663644806-22.01169473624.03289255713
50.115352468407-0.07535749882460.0984277940390.2354182901240.118055282440.2634562003350.0621515689784-0.07975853318930.05363681442590.128877647715-0.0173984474084-0.0257460624611-0.02337710455490.0387667539257-1.94395521335E-50.173552267684-0.023652594046-0.001048412689310.1744130293790.009443222068260.1579437455313.60873657754-23.932811727614.111678438
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 156 through 215 )
2X-RAY DIFFRACTION2chain 'A' and (resid 216 through 245 )
3X-RAY DIFFRACTION3chain 'A' and (resid 16 through 90 )
4X-RAY DIFFRACTION4chain 'A' and (resid 91 through 123 )
5X-RAY DIFFRACTION5chain 'A' and (resid 124 through 155 )

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