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- PDB-1kug: Crystal Structure of a Taiwan Habu Venom Metalloproteinase comple... -

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Basic information

Entry
Database: PDB / ID: 1kug
TitleCrystal Structure of a Taiwan Habu Venom Metalloproteinase complexed with its endogenous inhibitor pENW
Components
  • ENW
  • metalloproteinase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / alpha/beta protein / retro-binding manner / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / toxin activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Disintegrin, conserved site / Disintegrins signature. / Peptidase M12B, propeptide / Reprolysin family propeptide / Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain ...Disintegrin, conserved site / Disintegrins signature. / Peptidase M12B, propeptide / Reprolysin family propeptide / Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily / 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
: / Zinc metalloproteinase/disintegrin
Similarity search - Component
Biological speciesProtobothrops mucrosquamatus (Chinese habu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsHuang, K.F. / Chiou, S.H. / Ko, T.P. / Wang, A.H.J.
Citation
Journal: Eur.J.Biochem. / Year: 2002
Title: Determinants of the inhibition of a Taiwan habu venom metalloproteinase by its endogenous inhibitors revealed by X-ray crystallography and synthetic inhibitor analogues.
Authors: Huang, K.F. / Chiou, S.H. / Ko, T.P. / Wang, A.H.
#1: Journal: Biochem.Biophys.Res.Commun. / Year: 1995
Title: Characterization of multiple metalloproteinases with fibrinogenolytic activity from the venom of Taiwan habu (Trimeresurus mucrosquamatus): protein microsequencing coupled with cDNA sequence analysis.
Authors: Huang, K.F. / Hung, C.C. / pan, F.M. / Chow, L.P. / Tsugita, A. / Chiou, S.H.
History
DepositionJan 22, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 1.3Apr 16, 2014Group: Refinement description
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: metalloproteinase
B: ENW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,03113
Polymers23,7942
Non-polymers1,23711
Water11,349630
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-45 kcal/mol
Surface area9220 Å2
MethodPISA
2
A: metalloproteinase
B: ENW
hetero molecules

A: metalloproteinase
B: ENW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,06226
Polymers47,5894
Non-polymers2,47322
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area3770 Å2
ΔGint-116 kcal/mol
Surface area18180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.151, 61.151, 131.193
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-990-

CD

21A-617-

HOH

31B-853-

HOH

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Components

#1: Protein metalloproteinase / / Atrolysin e


Mass: 23364.824 Da / Num. of mol.: 1 / Fragment: CATALYTIC PROTEASE DOMAIN / Source method: isolated from a natural source
Source: (natural) Protobothrops mucrosquamatus (Chinese habu)
References: UniProt: O57413, EC: 3.4.24.44
#2: Protein/peptide ENW


Mass: 429.427 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The inhibitor pENW was synthesized by solid-phase method.
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 630 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG400, sodium acetate, cadmium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.1 M1reservoirCdCl2
20.1 Msodium acetate1reservoir
330 %(v/v)PEG4001reservoirpH4.6
410.5 mg/mlprotein1drop
50.2 Mammonium acetate1droppH6.0
6synthetic inhibitor1drop0.0005ml

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL17B2 / Wavelength: 1.08 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Dec 21, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.37→30 Å / Num. all: 121022 / Num. obs: 49996 / % possible obs: 93.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.9
Reflection shellResolution: 1.37→1.42 Å / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4604 / % possible all: 88.1
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 121022 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 88.1 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→30 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.202 2404 random
Rwork0.172 --
all-48075 -
obs-45671 -
Refinement stepCycle: LAST / Resolution: 1.37→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1646 0 11 630 2287
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.66
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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