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- PDB-5mnm: Cationic trypsin in complex with benzylamine (at 295 K) -

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Basic information

Entry
Database: PDB / ID: 5mnm
TitleCationic trypsin in complex with benzylamine (at 295 K)
ComponentsCationic trypsin
KeywordsHYDROLASE / hydrogen bonding / protonation / protein-ligand interaction
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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine 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
BENZYLAMINE / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsSchiebel, J. / Heine, A. / Klebe, G.
Funding support1items
OrganizationGrant numberCountry
European Research Council268145-DrugProfilBind
CitationJournal: to be published
Title: Cationic trypsin in complex with benzylamine (at 295 K)
Authors: Schiebel, J. / Heine, A. / Klebe, G.
History
DepositionDec 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)23,7606
Polymers23,3241
Non-polymers4355
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-43 kcal/mol
Surface area8940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.841, 58.334, 67.781
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ABN / BENZYLAMINE


Mass: 107.153 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9N
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
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: 2.32 Å3/Da / Density % sol: 47.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5, 15.5-16.5% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.8266 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 0.98→44.215 Å / Num. obs: 124579 / % possible obs: 99.6 % / Redundancy: 6.403 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 19.99
Reflection shellResolution: 0.98→1.04 Å / Redundancy: 6.184 % / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 4.18 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(dev_2429)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I8H

4i8h


Resolution: 0.98→17.437 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 7.88
RfactorNum. reflection% reflectionSelection details
Rfree0.1123 6224 5 %Random selection
Rwork0.1005 ---
obs0.1011 124484 99.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.98→17.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1614 0 24 145 1783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081900
X-RAY DIFFRACTIONf_angle_d1.0832634
X-RAY DIFFRACTIONf_dihedral_angle_d13.342703
X-RAY DIFFRACTIONf_chiral_restr0.096290
X-RAY DIFFRACTIONf_plane_restr0.008354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.98-0.99120.19991960.20773721X-RAY DIFFRACTION95
0.9912-1.00280.2042040.1913881X-RAY DIFFRACTION100
1.0028-1.01510.19442060.17353913X-RAY DIFFRACTION100
1.0151-1.02790.15462060.15233923X-RAY DIFFRACTION100
1.0279-1.04140.15362050.13413886X-RAY DIFFRACTION100
1.0414-1.05570.13512060.12013922X-RAY DIFFRACTION100
1.0557-1.07080.13372050.1093896X-RAY DIFFRACTION100
1.0708-1.08670.1162050.10013882X-RAY DIFFRACTION100
1.0867-1.10370.10422070.08763937X-RAY DIFFRACTION100
1.1037-1.12180.08672050.07823895X-RAY DIFFRACTION100
1.1218-1.14120.07622080.07433942X-RAY DIFFRACTION100
1.1412-1.16190.09062040.06883909X-RAY DIFFRACTION100
1.1619-1.18420.07622050.07113891X-RAY DIFFRACTION100
1.1842-1.20840.08812080.06863953X-RAY DIFFRACTION100
1.2084-1.23470.08082060.06963902X-RAY DIFFRACTION100
1.2347-1.26340.08542080.06633948X-RAY DIFFRACTION100
1.2634-1.2950.07682070.06773930X-RAY DIFFRACTION100
1.295-1.330.08192070.06643931X-RAY DIFFRACTION100
1.33-1.36910.07852070.06693931X-RAY DIFFRACTION100
1.3691-1.41330.08322080.06893955X-RAY DIFFRACTION100
1.4133-1.46380.08252080.06893944X-RAY DIFFRACTION100
1.4638-1.52230.08722090.06823971X-RAY DIFFRACTION100
1.5223-1.59160.08312070.07083942X-RAY DIFFRACTION100
1.5916-1.67540.0852080.07493989X-RAY DIFFRACTION100
1.6754-1.78030.09822110.08033991X-RAY DIFFRACTION100
1.7803-1.91760.09242080.08943955X-RAY DIFFRACTION100
1.9176-2.11030.10972120.09124029X-RAY DIFFRACTION100
2.1103-2.4150.10592120.1014017X-RAY DIFFRACTION100
2.415-3.040.13092140.13184059X-RAY DIFFRACTION100
3.04-17.43970.152220.13064215X-RAY DIFFRACTION100

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