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- PDB-1a5i: CATALYTIC DOMAIN OF VAMPIRE BAT (DESMODUS ROTUNDUS) SALIVA PLASMI... -

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Basic information

Entry
Database: PDB / ID: 1a5i
TitleCATALYTIC DOMAIN OF VAMPIRE BAT (DESMODUS ROTUNDUS) SALIVA PLASMINOGEN ACTIVATOR IN COMPLEX WITH EGR-CMK (GLU-GLY-ARG CHLOROMETHYL KETONE)
ComponentsPLASMINOGEN ACTIVATOR
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE / FIBRINOLYTIC ENZYMES / PLASMINOGEN ACTIVATORS / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


t-plasminogen activator / smooth muscle cell migration / plasminogen activation / platelet-derived growth factor receptor signaling pathway / serine-type endopeptidase activity / calcium ion binding / extracellular space
Similarity search - Function
Tissue plasminogen activator / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / EGF-like domain / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Kringle domain ...Tissue plasminogen activator / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / EGF-like domain / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / : / Kringle-like fold / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / 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 / 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
GLU-GLY-ARG-CHLOROMETHYL KETONE / Chem-0GJ / Salivary plasminogen activator alpha 1
Similarity search - Component
Biological speciesDesmodus rotundus (common vampire bat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsRenatus, M. / Stubbs, M.T. / Bode, W.
Citation
Journal: Biochemistry / Year: 1997
Title: Catalytic domain structure of vampire bat plasminogen activator: a molecular paradigm for proteolysis without activation cleavage.
Authors: Renatus, M. / Stubbs, M.T. / Huber, R. / Bringmann, P. / Donner, P. / Schleuning, W.D. / Bode, W.
#1: Journal: Embo J. / Year: 1997
Title: Lysine 156 Promotes the Anomalous Proenzyme Activity of Tpa: X-Ray Crystal Structure of Single-Chain Human Tpa
Authors: Renatus, M. / Engh, R.A. / Stubbs, M.T. / Huber, R. / Fischer, S. / Kohnert, U. / Bode, W.
#2: Journal: Curr.Opin.Struct.Biol. / Year: 1997
Title: Tissue-Type Plasminogen Activator: Variants and Crystal/Solution Structures Demarcate Structural Determinants of Function
Authors: Bode, W. / Renatus, M.
#3: Journal: J.Mol.Biol. / Year: 1996
Title: The 2.3 A Crystal Structure of the Catalytic Domain of Recombinant Two-Chain Human Tissue-Type Plasminogen Activator
Authors: Lamba, D. / Bauer, M. / Huber, R. / Fischer, S. / Rudolph, R. / Kohnert, U. / Bode, W.
History
DepositionFeb 17, 1998Processing site: BNL
Revision 1.0Mar 23, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 1.3Dec 12, 2012Group: Other
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: PLASMINOGEN ACTIVATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1122
Polymers29,7171
Non-polymers3961
Water59433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.860, 73.860, 135.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PLASMINOGEN ACTIVATOR


Mass: 29716.600 Da / Num. of mol.: 1 / Fragment: UNP residues 213-477
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desmodus rotundus (common vampire bat) / Organ: SALIVARY GLANDS / Cell line (production host): BHK / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P98119, t-plasminogen activator
#2: Chemical ChemComp-0GJ / L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 395.862 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28ClN6O5 / References: GLU-GLY-ARG-CHLOROMETHYL KETONE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE UNBOUND FORM OF THE INHIBITOR IS GLU-GLY-ARG-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN IT ...THE UNBOUND FORM OF THE INHIBITOR IS GLU-GLY-ARG-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN IT FORMS TWO COVALENT BONDS: 1) A COVALENT BOND TO SER 195 FORMING A HEMIKETAL AR7 AND 2) A COVALENT BOND TO NE2 OF HIS 57
Sequence detailsTHE PROTEIN IS A DELETION MUTANT OF FULL-LENGTH DSPAALPHA1 (P98119) CONSISTING OF A SIGNAL PEPTIDE ...THE PROTEIN IS A DELETION MUTANT OF FULL-LENGTH DSPAALPHA1 (P98119) CONSISTING OF A SIGNAL PEPTIDE (THREE RESIDUES) AND THE CATALYTIC DOMAIN OF FULL LENGTH-DSPAALPHA1. THE FINGER-, EGF- AND KRINGEL-DOMAIN ARE MISSING. IT IS THEREFORE ALSO CALLED (DELTAFEK) DSPAALPHA1. THE RESIDUE NUMBERING GIVEN WITH THE COORDINATE SET HAS BEEN DERIVED FROM THE TOPOLOGY EQUIVALENCE TO CHYMOTRYPSINOGEN (SEE REFERENCE 1).

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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: 3.58 Å3/Da / Density % sol: 65.66 %
Crystal growpH: 9 / Details: pH 9.0
Crystal
*PLUS
Density % sol: 59 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop / PH range low: 9.2 / PH range high: 8.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 %PEG80001reservoir
20.1 MMes/Tris1reservoir

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 18, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→25 Å / Num. obs: 9582 / % possible obs: 97.2 % / Observed criterion σ(I): 3 / Redundancy: 2.3 % / Biso Wilson estimate: 65.48 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 3.51
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 1.9 / % possible all: 97.9
Reflection
*PLUS
Num. measured all: 22337
Reflection shell
*PLUS
% possible obs: 97.9 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
X-PLOR3.851model building
X-PLOR3.851refinement
CCP4(ROTAVATA)data scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RTF

1rtf


Resolution: 2.9→7 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.198 --
obs0.198 8624 94.2 %
Displacement parametersBiso mean: 29 Å2
Refinement stepCycle: LAST / Resolution: 2.9→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2083 0 25 33 2141
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.673
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.93
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.302
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.657
X-RAY DIFFRACTIONx_mcangle_it5.967
X-RAY DIFFRACTIONx_scbond_it5.003
X-RAY DIFFRACTIONx_scangle_it7.457
LS refinement shellResolution: 2.9→3 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rwork0.3489 835 -
obs--94 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.93
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.302
LS refinement shell
*PLUS
Rfactor obs: 0.3489

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