3AYU Hydrolase Hydrolase Inhibitor date May 17, 2011
title Crystal Structure Of Mmp-2 Active Site Mutant In Complex Wit Drived Decapeptide Inhibitor
authors H.Hashimoto, T.Takeuchi, K.Komatsu, K.Miyazaki, M.Sato, S.Higashi
compound source
Molecule: 72 Kda Type Iv Collagenase
Chain: A
Fragment: Unp Residues 110-219 And 394-450
Synonym: 72 Kda Gelatinase, Gelatinase A, Matrix Metallopro Mmp-2;
Ec: 3.4.24.24
Engineered: Yes
Mutation: Yes
Other_details: Fusion Protein Of Unp Residues 110-219 And 3 From 72 Kda Type Iv Collagenase;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mmp2, Clg4a
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Dh5alpha
Expression_system_vector_type: Vector
Expression_system_vector: Pflag-Ctc

Molecule: Amyloid Beta A4 Protein
Chain: B
Fragment: Unp Residues 586-595
Synonym: Abpp, Appi, App, Alzheimer Disease Amyloid Protein Vascular Amyloid Peptide, Cvap, Prea4, Protease Nexin-II, P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Synthetic Peptide
symmetry Space Group: P 21 21 21
R_factor 0.160 R_Free 0.205
crystal
cell
length a length b length c angle alpha angle beta angle gamma
61.881 76.060 37.082 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand CA, ZN enzyme Hydrolase E.C.3.4.24.24 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural basis for matrix metalloproteinase-2 (MMP-2)-selective inhibitory action of {beta}-amyloid precursor protein-derived inhibitor., Hashimoto H, Takeuchi T, Komatsu K, Miyazaki K, Sato M, Higashi S, J Biol Chem. 2011 Aug 3. PMID:21813640
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (65 Kb) [Save to disk]
  • Biological Unit Coordinates (3ayu.pdb1.gz) 60 Kb
  • LPC: Ligand-Protein Contacts for 3AYU
  • CSU: Contacts of Structural Units for 3AYU
  • Structure Factors (171 Kb)
  • Retrieve 3AYU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3AYU from S2C, [Save to disk]
  • Re-refined 3ayu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3AYU in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3AYU
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3AYU, from MSDmotif at EBI
  • Fold representative 3ayu from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ayu_A] [3ayu_B] [3ayu]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3AYU: [ZnMc ] by SMART
  • Other resources with information on 3AYU
  • Community annotation for 3AYU at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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