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
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
  • Alignments of the sequence of 3AYU with the sequences similar proteins can be viewed for 3AYU's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • 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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