1D5J Hydrolase date Oct 07, 1999
title Crystal Structure Of Mmp3 Complexed With A Thiazepine Based
authors N.G.Almstead, R.S.Bradley, S.Pikul, B.De, M.G.Natchus
compound source
Molecule: Stromelysin-1
Chain: A, B
Fragment: Catalytic Domain
Synonym: Mmp-3
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
symmetry Space Group: P 21 21 21
R_factor 0.237 R_Free 0.257
length a length b length c angle alpha angle beta angle gamma
37.780 78.540 105.270 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand CA, MM3, ZN enzyme Hydrolase E.C. BRENDA
related structures by homologous chain: 1C8T, 1EAK, 1UEA
A, B

Primary referenceDesign, synthesis, and biological evaluation of potent thiazine- and thiazepine-based matrix metalloproteinase inhibitors., Almstead NG, Bradley RS, Pikul S, De B, Natchus MG, Taiwo YO, Gu F, Williams LE, Hynd BA, Janusz MJ, Dunaway CM, Mieling GE, J Med Chem 1999 Nov 4;42(22):4547-62. PMID:10579818
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (65 Kb) [Save to disk]
  • Biological Unit Coordinates (1d5j.pdb1.gz) 30 Kb
  • Biological Unit Coordinates (1d5j.pdb2.gz) 31 Kb
  • LPC: Ligand-Protein Contacts for 1D5J
  • CSU: Contacts of Structural Units for 1D5J
  • Likely Quarternary Molecular Structure file(s) for 1D5J
  • Retrieve 1D5J in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1D5J from S2C, [Save to disk]
  • View 1D5J 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 1D5J
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1D5J, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1d5ja_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1d5jb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1d5j from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1d5j] [1d5j_B] [1d5j_A]
  • SWISS-PROT database: [P08254]
  • Domain organization of [MMP3_HUMAN] by SWISSPFAM
  • Domain found in 1D5J: [ZnMc ] by SMART
  • Other resources with information on 1D5J
  • Community annotation for 1D5J at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Domain movements in 1D5J from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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