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- PDB-1gec: GLYCYL ENDOPEPTIDASE-COMPLEX WITH BENZYLOXYCARBONYL-LEUCINE-VALIN... -

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Basic information

Entry
Database: PDB / ID: 1gec
TitleGLYCYL ENDOPEPTIDASE-COMPLEX WITH BENZYLOXYCARBONYL-LEUCINE-VALINE-GLYCINE-METHYLENE COVALENTLY BOUND TO CYSTEINE 25
Components
  • BENZYLOXYCARBONYL-LEUCINE-VALINE-GLYCINE-METHYLENE INHIBITOR
  • GLYCYL ENDOPEPTIDASE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


glycyl endopeptidase / cysteine-type peptidase activity
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
BENZYLOXYCARBONYL-LEUCINE-VALINE-GLYCINE-METHYLENE / Papaya proteinase 4
Similarity search - Component
Biological speciesCarica papaya (papaya)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsOhara, B.P. / Hemmings, A.M. / Buttle, D.J. / Pearl, L.H.
CitationJournal: Biochemistry / Year: 1995
Title: Crystal structure of glycyl endopeptidase from Carica papaya: a cysteine endopeptidase of unusual substrate specificity.
Authors: O'Hara, B.P. / Hemmings, A.M. / Buttle, D.J. / Pearl, L.H.
History
DepositionMay 25, 1995Processing site: BNL
Revision 1.0Dec 7, 1995Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: GLYCYL ENDOPEPTIDASE
I: BENZYLOXYCARBONYL-LEUCINE-VALINE-GLYCINE-METHYLENE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)23,8082
Polymers23,8082
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.780, 55.780, 64.430
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein GLYCYL ENDOPEPTIDASE


Mass: 23344.162 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Carica papaya (papaya) / References: UniProt: P05994, glycyl endopeptidase
#2: Protein/peptide BENZYLOXYCARBONYL-LEUCINE-VALINE-GLYCINE-METHYLENE INHIBITOR


Type: Peptide-like / Class: Inhibitor / Mass: 463.958 Da / Num. of mol.: 1 / Source method: obtained synthetically
References: BENZYLOXYCARBONYL-LEUCINE-VALINE-GLYCINE-METHYLENE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal grow
*PLUS
pH: 5.6 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
121.7 mg/mlglycyl endopeptidase11
23.2 M11NaCl
350 mMsodium acetate11

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.1 Å / Num. obs: 14026 / % possible obs: 97.4 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.05
Reflection
*PLUS
Highest resolution: 2.1 Å / Rmerge(I) obs: 0.05

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Processing

Software
NameClassification
MOSFLMdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.1→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.258 -5 %
Rwork0.196 --
obs0.196 12725 -
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1672 0 0 117 1789
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg2.2
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_improper_angle_deg / Dev ideal: 1.9

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