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- PDB-2wuc: Crystal structure of HGFA in complex with the allosteric non- inh... -

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Basic information

Entry
Database: PDB / ID: 2wuc
TitleCrystal structure of HGFA in complex with the allosteric non- inhibitory antibody Fab40.deltaTrp and Ac-KQLR-chloromethylketone
Components
  • (FAB FRAGMENT FAB40.DELTATRP ...) x 2
  • (HEPATOCYTE GROWTH FACTOR ACTIVATOR ...) x 2
  • ACE-KQLR-CHLOROMETHYLKETONE INHIBITOR
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE / EGF-LIKE DOMAIN / ALLOSTERIC INHIBITOR / KRINGLE / ANTIBODY / HYDROLASE / FAB COMPLEX / GLYCOPROTEIN / IMMUNE SYSTEM / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


MET Receptor Activation / zymogen activation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / rough endoplasmic reticulum / serine-type peptidase activity / blood coagulation / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / cytosol
Similarity search - Function
Coagulation factor XII/hepatocyte growth factor activator / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. ...Coagulation factor XII/hepatocyte growth factor activator / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / EGF-like domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Epidermal growth factor-like domain. / Kringle-like fold / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / 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 / Thrombin, subunit H / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
N-acetyl-6-ammonio-L-norleucyl-L-glutaminyl-N-[(1S)-4-{[amino(iminio)methyl]amino}-1-(chloroacetyl)butyl]-L-leucinamide / Hepatocyte growth factor activator
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGanesan, R. / Eigenbrot, C. / Shia, S.
CitationJournal: Structure / Year: 2009
Title: Unraveling the Allosteric Mechanism of Serine Protease Inhibition by an Antibody
Authors: Ganesan, R. / Eigenbrot, C. / Wu, Y. / Liang, W.C. / Shia, S. / Lipari, M.T. / Kirchhofer, D.
History
DepositionOct 1, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Jun 6, 2012Group: Other
Revision 1.3Mar 6, 2013Group: Other
Revision 1.4Dec 21, 2016Group: Source and taxonomy
Revision 2.0Jul 1, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.type / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEPATOCYTE GROWTH FACTOR ACTIVATOR LONG CHAIN
B: HEPATOCYTE GROWTH FACTOR ACTIVATOR SHORT CHAIN
H: FAB FRAGMENT FAB40.DELTATRP HEAVY CHAIN
I: ACE-KQLR-CHLOROMETHYLKETONE INHIBITOR
L: FAB FRAGMENT FAB40.DELTATRP LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7996
Polymers79,3755
Non-polymers4241
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8190 Å2
ΔGint-33.8 kcal/mol
Surface area28360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.359, 147.889, 146.371
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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HEPATOCYTE GROWTH FACTOR ACTIVATOR ... , 2 types, 2 molecules AB

#1: Protein HEPATOCYTE GROWTH FACTOR ACTIVATOR LONG CHAIN


Mass: 27982.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-GLYCOSYLATION AT ASN74 / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: TRICHOPLUSIA NI (cabbage looper)
References: UniProt: Q04756, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide HEPATOCYTE GROWTH FACTOR ACTIVATOR SHORT CHAIN


Mass: 3962.654 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: TRICHOPLUSIA NI (cabbage looper)
References: UniProt: Q04756, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

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Antibody , 2 types, 2 molecules HL

#3: Antibody FAB FRAGMENT FAB40.DELTATRP HEAVY CHAIN


Mass: 23584.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): 33D3
#5: Antibody FAB FRAGMENT FAB40.DELTATRP LIGHT CHAIN


Mass: 23238.748 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): 33D3

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Protein/peptide / Sugars / Non-polymers , 3 types, 133 molecules I

#4: Protein/peptide ACE-KQLR-CHLOROMETHYLKETONE INHIBITOR


Type: Peptide-like / Class: Inhibitor / Mass: 606.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
References: N-acetyl-6-ammonio-L-norleucyl-L-glutaminyl-N-[(1S)-4-{[amino(iminio)methyl]amino}-1-(chloroacetyl)butyl]-L-leucinamide
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE UNBOUND FORM OF THE INHIBITOR IS ACE-KQLR-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN IT ...THE UNBOUND FORM OF THE INHIBITOR IS ACE-KQLR-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

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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: 2.92 Å3/Da / Density % sol: 57.55 %
Crystal growpH: 7.2 / Details: 14% PEG 10,000, 100 MM HEPES PH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97607
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97607 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 24263 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Biso Wilson estimate: 48.4 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 15
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.9 / % possible all: 97.3

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WUB

2wub


Resolution: 2.7→19.93 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2076852.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.274 2388 9.9 %RANDOM
Rwork0.226 ---
obs0.226 24111 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.22 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 38.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.23 Å20 Å20 Å2
2---5.28 Å20 Å2
3---7.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5160 0 28 131 5319
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.396 370 9.6 %
Rwork0.322 3498 -
obs--96.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4NAG.PARNAG.TOP
X-RAY DIFFRACTION5MAI.PARMAI.TOP

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