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- PDB-1ekb: THE SERINE PROTEASE DOMAIN OF ENTEROPEPTIDASE BOUND TO INHIBITOR ... -

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Basic information

Entry
Database: PDB / ID: 1ekb
TitleTHE SERINE PROTEASE DOMAIN OF ENTEROPEPTIDASE BOUND TO INHIBITOR VAL-ASP-ASP-ASP-ASP-LYS-CHLOROMETHANE
Components
  • (ENTEROPEPTIDASE) x 2
  • VAL-ASP-ASP-ASP-ASP-LYK PEPTIDE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ENTEROPEPTIDASE / TRYPSINOGEN ACTIVATION / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


protein digestion / enteropeptidase / trypsinogen activation / scavenger receptor activity / membrane => GO:0016020 / serine-type endopeptidase activity / membrane
Similarity search - Function
Peptidase S1A, enteropeptidase / SRCR domain signature. / Scavenger receptor cysteine-rich domain / Domain found in sea urchin sperm protein, enterokinase, agrin / SRCR domain / SRCR domain profile. / MAM domain signature. / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich ...Peptidase S1A, enteropeptidase / SRCR domain signature. / Scavenger receptor cysteine-rich domain / Domain found in sea urchin sperm protein, enterokinase, agrin / SRCR domain / SRCR domain profile. / MAM domain signature. / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SEA domain superfamily / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / SEA domain profile. / SEA domain / SEA domain / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / 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 / Concanavalin A-like lectin/glucanase domain superfamily / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFuetterer, K. / Lu, D. / Sadler, J.E. / Waksman, G.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of enteropeptidase light chain complexed with an analog of the trypsinogen activation peptide.
Authors: Lu, D. / Futterer, K. / Korolev, S. / Zheng, X. / Tan, K. / Waksman, G. / Sadler, J.E.
History
DepositionMay 2, 1999Deposition site: BNL / Processing site: NDB
Revision 1.0Oct 14, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.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: ENTEROPEPTIDASE
B: ENTEROPEPTIDASE
C: VAL-ASP-ASP-ASP-ASP-LYK PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5745
Polymers28,4443
Non-polymers1312
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-59 kcal/mol
Surface area10270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.990, 70.650, 85.220
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/peptide ENTEROPEPTIDASE / / E.C.3.4.21.9 / ENTEROKINASE / HEAVY CHAIN


Mass: 1419.708 Da / Num. of mol.: 1
Fragment: 13-AMINO ACID REMNANT OF AMINO TERMINAL DOMAIN OF HEAVY CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Plasmid: PETL / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P98072, enteropeptidase
#2: Protein ENTEROPEPTIDASE / / E.C.3.4.21.9 / ENTEROKINASE / LIGHT CHAIN


Mass: 26283.785 Da / Num. of mol.: 1 / Fragment: SERINE PROTEASE DOMAIN OR LIGHT CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Plasmid: PETL / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P98072, enteropeptidase
#3: Protein/peptide VAL-ASP-ASP-ASP-ASP-LYK PEPTIDE


Mass: 740.158 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Compound detailsVAL-ASP-ASP-ASP-ASP-LYK-CHLOROMETHANE (CHAIN C) HAS FORMED CONNECTIONS TO ENTEROPETPIDASE: 1) VIA A ...VAL-ASP-ASP-ASP-ASP-LYK-CHLOROMETHANE (CHAIN C) HAS FORMED CONNECTIONS TO ENTEROPETPIDASE: 1) VIA A HEMIKETAL GROUP FROM FROM C OF LYK C 306 TO OG OF SER B 195. 2) VIA A METHYLENE GROUP FROM 0QE C 307 TO NE2 OF HIS B 57.

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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: 2.12 Å3/Da / Density % sol: 40 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / pH: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMsodium cacodylate1reservoirpH5.0
210 mMzinc sulfate1reservoir
310 %(w/v)PEG4001reservoir
44 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 15, 1998
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 10541 / % possible obs: 92.6 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 10
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2 % / Rmerge(I) obs: 0.088 / Mean I/σ(I) obs: 3 / Rsym value: 0.088 / % possible all: 89.2
Reflection
*PLUS
Num. measured all: 28051
Reflection shell
*PLUS
% possible obs: 89.2 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GCD

1gcd


Resolution: 2.3→30 Å / Rfactor Rfree error: 0.012 / Data cutoff high rms absF: 354608.98 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.269 546 4.9 %RANDOM
Rwork0.234 ---
obs-10400 92.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.18 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso mean: 23.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 2 108 2021
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.042
X-RAY DIFFRACTIONc_scbond_it2.472
X-RAY DIFFRACTIONc_scangle_it32.5
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.367 70 5.8 %
Rwork0.295 1142 -
obs--88.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP_CH2.PARAMPROTEIN_CH2.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 4.9 % / Rfactor obs: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.367 / % reflection Rfree: 5.8 % / Rfactor Rwork: 0.295

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