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- PDB-3aig: ADAMALYSIN II WITH PEPTIDOMIMETIC INHIBITOR POL656 -

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Basic information

Entry
Database: PDB / ID: 3aig
TitleADAMALYSIN II WITH PEPTIDOMIMETIC INHIBITOR POL656
ComponentsADAMALYSIN IIAdamalysin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SNAKE VENOM METALLOENDOPETIDASE / ZINC PROTEASE / METALLOPROTEASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


adamalysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
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
Furoyl-LeusycloTrp; Po1656 / Chem-0ZC / : / Snake venom metalloproteinase adamalysin-2
Similarity search - Component
Biological speciesCrotalus adamanteus (eastern diamondback rattlesnake)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.8 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 25, 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 2.0Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Polymer sequence / Refinement description
Category: database_2 / entity_poly ...database_2 / entity_poly / 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 / _entity_poly.pdbx_seq_one_letter_code_can / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADAMALYSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7785
Polymers23,1521
Non-polymers6254
Water2,324129
1
A: ADAMALYSIN II
hetero molecules

A: ADAMALYSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,55510
Polymers46,3052
Non-polymers1,2508
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556x,x-y,-z+11
Unit cell
Length a, b, c (Å)73.550, 73.550, 96.670
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 A

#1: Protein ADAMALYSIN II / Adamalysin


Mass: 23152.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Crotalus adamanteus (eastern diamondback rattlesnake)
Secretion: VENOM
References: GenBank: 547144, UniProt: P34179*PLUS, adamalysin

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Non-polymers , 5 types, 133 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-0ZC / (3R)-2-[N-(furan-2-ylcarbonyl)-L-leucyl]-2,3,4,9-tetrahydro-1H-beta-carboline-3-carboxylic acid / Furoyl-LeusycloTrp / Po1656


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 423.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H25N3O5 / References: Furoyl-LeusycloTrp; Po1656
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE SEQUENCE USED IN THIS ENTRY WAS DETERMINED BY A COMBINATION OF CHEMICAL AND X-RAY SEQUENCING.
Source detailsTHE N-TERMINUS WAS BLOCKED AGAINST AMINOPEPTIDASE ACTIVITY BY GLUTAMINE CYCLIZATION TO RENDER ...THE N-TERMINUS WAS BLOCKED AGAINST AMINOPEPTIDASE ACTIVITY BY GLUTAMINE CYCLIZATION TO RENDER PYROGLUTAMATE. THIS RESIDUE WAS NOT MODELLED 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: 3.26 Å3/Da / Density % sol: 62.22 %
Crystal growDetails: 1.8 M AMMONIUM SULFATE
Crystal grow
*PLUS
pH: 5 / Method: unknown / Details: Gomis-Ruth, F.X., (1993) Embo J., 12, 4151.
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: 2.5→20 Å / Num. obs: 8311 / % possible obs: 78.9 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 4.4
Reflection shellResolution: 2.5→2.63 Å / % possible all: 45.7
Reflection
*PLUS
Num. measured all: 18531
Reflection shell
*PLUS
% possible obs: 45.7 % / Redundancy: 1.7 % / Num. unique obs: 680 / Num. measured obs: 1153 / Rmerge(I) obs: 0.32

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Processing

Software
NameVersionClassification
MADNESdata collection
ABSCORR/CCP4data reduction
X-PLOR3.1model building
X-PLOR3.1refinement
MADNESdata reduction
ABSCORRdata scaling
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: NATIVE ADAMALYSIN II (PDB ENTRY 1IAG)

1iag


Resolution: 2.8→7 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.194 -
obs0.194 5926
Refinement stepCycle: LAST / Resolution: 2.8→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1616 0 38 129 1783
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.3
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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