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- PDB-1v6d: The crystal structure of the trypsin complex with synthetic heter... -

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Basic information

Entry
Database: PDB / ID: 1v6d
TitleThe crystal structure of the trypsin complex with synthetic heterochiral peptide
Components
  • PD(AIB)L(AIB)LA
  • Trypsin
KeywordsHYDROLASE / Trypsin complex / synthetic peptide
Function / homology
Function and homology information


trypsin / digestion / 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
ACETATE ION / METHYLAMINE / TERT-BUTYL FORMATE / Trypsin
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsShamaladevi, N. / Pattabhi, V.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2005
Title: Secondary binding site of trypsin: revealed by crystal structure of trypsin-peptide complex.
Authors: Shamaladevi, N. / Pattabhi, V.
History
DepositionNov 28, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 6, 2019Group: Data collection / Database references / Derived calculations
Category: citation / struct_conn
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.title / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Oct 25, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trypsin
B: PD(AIB)L(AIB)LA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4246
Polymers24,1912
Non-polymers2324
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.930, 53.719, 77.473
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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

#1: Protein Trypsin


Mass: 23493.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P00761, trypsin
#2: Protein/peptide PD(AIB)L(AIB)LA


Mass: 697.821 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: A heterochiral heptapeptide synthesized chemically.

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Non-polymers , 5 types, 164 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-TBF / TERT-BUTYL FORMATE / TERTIARY BUTOXY CARBONYL


Mass: 102.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O2
#6: Chemical ChemComp-NME / METHYLAMINE


Mass: 31.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH5N
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE NUMBERING ASSIGNED IN THE COORDINATE FILE IS ACCORDING TO CHYMOTRYPSIN NUMBERING IN ORDER TO ...THE NUMBERING ASSIGNED IN THE COORDINATE FILE IS ACCORDING TO CHYMOTRYPSIN NUMBERING IN ORDER TO MAINTAIN THE ACTIVE SITE RESIDUES NUMBER SAME IN THE SERINE FAMILY. NO RESIDUES ARE MISSING IN THE STRUCTURE DUE TO LACK OF DENSITY.

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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: 1.87 Å3/Da / Density % sol: 33.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 2M ammonium sulphate, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 9, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→44.28 Å / Num. all: 15129 / Num. obs: 15129 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Rmerge(I) obs: 0.069
Reflection shellResolution: 1.9→1.97 Å / Num. unique all: 15129 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QQU

1qqu


Resolution: 1.9→44.28 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.848 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.159 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17849 740 4.9 %RANDOM
Rwork0.15324 ---
all0.15453 14361 --
obs0.15453 14361 94.28 %-
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: 17.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å20 Å2
2--0.33 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1690 0 12 162 1864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0211738
X-RAY DIFFRACTIONr_bond_other_d0.0020.021511
X-RAY DIFFRACTIONr_angle_refined_deg3.5541.962341
X-RAY DIFFRACTIONr_angle_other_deg1.95633545
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2713218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.0415290
X-RAY DIFFRACTIONr_chiral_restr0.1420.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021883
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02305
X-RAY DIFFRACTIONr_nbd_refined0.420.3416
X-RAY DIFFRACTIONr_nbd_other0.2520.31576
X-RAY DIFFRACTIONr_nbtor_other0.2020.51
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2540.5197
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0650.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.8410.336
X-RAY DIFFRACTIONr_symmetry_vdw_other0.5360.374
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4270.514
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0680.51
X-RAY DIFFRACTIONr_mcbond_it1.3971.51140
X-RAY DIFFRACTIONr_mcangle_it2.54521790
X-RAY DIFFRACTIONr_scbond_it4.443598
X-RAY DIFFRACTIONr_scangle_it6.5274.5545
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.213 45
Rwork0.178 999

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