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- PDB-2aig: ADAMALYSIN II WITH PEPTIDOMIMETIC INHIBITOR POL647 -

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Basic information

Entry
Database: PDB / ID: 2aig
TitleADAMALYSIN II WITH PEPTIDOMIMETIC INHIBITOR POL647
ComponentsADAMALYSIN II
KeywordsHYDROLAST/HYDROLASE INHIBITOR / ZINC PROTEASE / METALLOENDOPETIDASE / COMPLEX OF METALLOPROTEASE-INHIBITOR / HYDROLAST-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


adamalysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-(furan-2-ylcarbonyl)-L-leucyl-L-tryptophan / N-(furan-2-ylcarbonyl)-L-leucyl-L-tryptophan / : / Snake venom metalloproteinase adamalysin-2
Similarity search - Component
Biological speciesCrotalus adamanteus (eastern diamondback rattlesnake)
MethodX-RAY DIFFRACTION / RIGID BODY / Resolution: 2.6 Å
AuthorsGomis-Rueth, F.X. / Meyer, E.F. / Kress, L.F. / Politi, V.
Citation
Journal: Protein Sci. / Year: 1998
Title: Structures of adamalysin II with peptidic inhibitors. Implications for the design of tumor necrosis factor alpha convertase inhibitors.
Authors: Gomis-Ruth, F.X. / Meyer, E.F. / Kress, L.F. / Politi, V.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Refined 2.0 A X-Ray Crystal Structure of the Snake Venom Zinc-Endopeptidase Adamalysin II. Primary and Tertiary Structure Determination, Refinement, Molecular Structure and Comparison with ...Title: Refined 2.0 A X-Ray Crystal Structure of the Snake Venom Zinc-Endopeptidase Adamalysin II. Primary and Tertiary Structure Determination, Refinement, Molecular Structure and Comparison with Astacin, Collagenase and Thermolysin
Authors: Gomis-Ruth, F.X. / Kress, L.F. / Kellermann, J. / Mayr, I. / Lee, X. / Huber, R. / Bode, W.
#2: Journal: Embo J. / Year: 1993
Title: First Structure of a Snake Venom Metalloproteinase: A Prototype for Matrix Metalloproteinases/Collagenases
Authors: Gomis-Ruth, F.X. / Kress, L.F. / Bode, W.
History
DepositionOct 12, 1997Processing site: BNL
Revision 1.0Apr 15, 1998Provider: 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 1.4Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.5Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 1.6Jul 10, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.7Oct 23, 2024Group: Structure summary / Category: 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
P: ADAMALYSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7925
Polymers23,1791
Non-polymers6134
Water2,972165
1
P: ADAMALYSIN II
hetero molecules

P: ADAMALYSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,58510
Polymers46,3592
Non-polymers1,2268
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556x,x-y,-z+11
2
P: ADAMALYSIN II
hetero molecules

P: ADAMALYSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,58510
Polymers46,3592
Non-polymers1,2268
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+y,y,-z+2/31
Buried area3690 Å2
ΔGint-134 kcal/mol
Surface area17400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.550, 73.550, 96.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

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Protein , 1 types, 1 molecules P

#1: Protein ADAMALYSIN II


Mass: 23179.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Crotalus adamanteus (eastern diamondback rattlesnake)
Secretion: VENOM / Tissue: VENOM
References: GenBank: 547144, UniProt: P34179*PLUS, adamalysin

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Non-polymers , 5 types, 169 molecules

#2: Chemical ChemComp-0GR / N-(furan-2-ylcarbonyl)-L-leucyl-L-tryptophan


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 411.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H25N3O5 / References: N-(furan-2-ylcarbonyl)-L-leucyl-L-tryptophan
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE N-TERMINUS WAS BLOCKED AGAINST AMINOPEPTIDASE ACTIVITY BY GLUTAMINE CYCLATION TO RENDER ...THE N-TERMINUS WAS BLOCKED AGAINST AMINOPEPTIDASE ACTIVITY BY GLUTAMINE CYCLATION TO RENDER PYROGLUTAMATE (PGA). THIS RESIDUE WAS NOT MODELLED DUE TO LACK OF DENSITY.
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: 3.19 Å3/Da / Density % sol: 61.49 %
Crystal growDetails: 1.8 M AMMONIUM SULFATE
Crystal grow
*PLUS
pH: 5 / Method: unknown / Details: Kurecki, T., (1978) J. Biol. Chem., 253, 8340.
Components of the solutions
*PLUS
Conc.: 1.8 M / Common name: ammonium sulfate

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER
RadiationMonochromator: NI-FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 11018 / % possible obs: 81.6 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 5.4
Reflection shellResolution: 2.3→2.42 Å / % possible all: 48.2
Reflection
*PLUS
Num. measured all: 27819
Reflection shell
*PLUS
% possible obs: 48.2 % / Redundancy: 1.6 % / Num. unique obs: 924 / Num. measured obs: 1486 / Rmerge(I) obs: 0.325

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Processing

Software
NameClassification
MADNESdata collection
ABSCORR/ABSURD/CCP4data reduction
X-PLORmodel building
X-PLORrefinement
MADNESdata reduction
ABSCORRdata scaling
ABSURDdata scaling
CCP4data scaling
X-PLORphasing
RefinementMethod to determine structure: RIGID BODY
Starting model: NATIVE ADAMALYSIN II (PDB ENTRY 1IAG)

1iag


Resolution: 2.6→7 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.191 -
obs0.191 7719
Refinement stepCycle: LAST / Resolution: 2.6→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1616 0 37 165 1818
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.23
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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