1D8F	Hydrolase	date	Oct 22, 1999
title	Crystal Structure Of Mmp3 Complexed With A Piperazine Based
authors	M.Y.Cheng, B.De, S.Pikul, N.G.Almstead, M.G.Natchus, M.V.Anastasi S.J.Mcphail, C.E.Snider, Y.O.Taiwo, L.Y.Chen
compound		source
Molecule: Stromelysin-1 Precursor Chain: A, B Fragment: Catalytic Domain Synonym: Mmp-3 Ec: 3.4.24.17 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Cell: Fibroblast Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 21 21 21	R_factor 0.294 R_Free 0.252
crystal cell	length a length b length c angle alpha angle beta angle gamma 38.270 78.540 106.580 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.40 Å
ligand	CA, SPI, ZN BindingDB	enzyme	Hydrolase E.C.3.4.24.17 BRENDA
related structures	by homologous chain: 1D8M, 456C
Gene Ontology	Chain Function Process Component A, B
Primary reference	Design and synthesis of piperazine-based matrix metalloproteinase inhibitors., Cheng M, De B, Pikul S, Almstead NG, Natchus MG, Anastasio MV, McPhail SJ, Snider CE, Taiwo YO, Chen L, Dunaway CM, Gu F, Dowty ME, Mieling GE, Janusz MJ, Wang-Weigand S, J Med Chem 2000 Feb 10;43(3):369-80. PMID:10669564

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (61 Kb) [Save to disk] Biological Unit Coordinates (1d8f.pdb1.gz) 28 Kb Biological Unit Coordinates (1d8f.pdb2.gz) 29 Kb LPC: Ligand-Protein Contacts for 1D8F CSU: Contacts of Structural Units for 1D8F Likely Quarternary Molecular Structure file(s) for 1D8F Retrieve 1D8F in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1D8F from S2C, [Save to disk]

View 1D8F 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 1D8F

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1D8F, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1d8fa_, region A [Jmol] [rasmolscript] [script source]     - Domain d1d8fb_, region B [Jmol] [rasmolscript] [script source] 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: [1d8f_B] [1d8f] [1d8f_A] SWISS-PROT database: [P08254] Domain organization of [MMP3_HUMAN] by SWISSPFAM Domain found in 1D8F: [ZnMc ] by SMART

Other resources with information on 1D8F

Community annotation for 1D8F at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Domain movements in 1D8F from the Database of Macromolecular Movements. Images from IMB Jena Image Library of Biological Macromolecules.

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