1DDJ	Blood Clotting	date	Nov 10, 1999
title	Crystal Structure Of Human Plasminogen Catalytic Domain
authors	X.Wang, S.Terzyan, J.Tang, J.Loy, X.Lin, X.Zhang
compound		source
Molecule: Plasminogen Chain: A, B, C, D Fragment: Catalytic Domain Ec: 3.4.21.7 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Tissue: Blood Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet11
symmetry	Space Group: P 1 21 1	R_factor 0.194 R_Free 0.267
crystal cell	length a length b length c angle alpha angle beta angle gamma 90.490 46.160 126.650 90.00 91.75 90.00
method	X-Ray Diffraction	resolution	2.00 Å
ligand		enzyme	Hydrolase E.C.3.4.21.7 BRENDA
related structures	by homologous chain: 1QRZ
Gene Ontology	Chain Function Process Component A, D, C, B serine-type endopeptidase ac... protein binding peptidase activity serine-type peptidase activi... hydrolase activity protein domain specific bind... apolipoprotein binding cell surface binding platelet degranulation proteolysis blood coagulation hemostasis negative regulation of cell ... negative regulation of cell-... extracellular matrix disasse... platelet activation extracellular matrix organiz... fibrinolysis cellular protein metabolic p... tissue remodeling negative regulation of fibri... positive regulation of fibri... negative regulation of cell-... extracellular region extracellular space plasma membrane platelet alpha granule lumen... extrinsic to external side o...
Primary reference	Human plasminogen catalytic domain undergoes an unusual conformational change upon activation., Wang X, Terzyan S, Tang J, Loy JA, Lin X, Zhang XC, J Mol Biol 2000 Jan 28;295(4):903-14. PMID:10656799

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (172 Kb) [Save to disk] Biological Unit Coordinates (1ddj.pdb1.gz) 44 Kb Biological Unit Coordinates (1ddj.pdb2.gz) 45 Kb Biological Unit Coordinates (1ddj.pdb3.gz) 44 Kb Biological Unit Coordinates (1ddj.pdb4.gz) 44 Kb CSU: Contacts of Structural Units for 1DDJ Likely Quarternary Molecular Structure file(s) for 1DDJ Retrieve 1DDJ in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1DDJ from S2C, [Save to disk]

View 1DDJ 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 1DDJ

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 1DDJ, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1ddja_, region A [Jmol] [rasmolscript] [script source]     - Domain d1ddjb_, region B [Jmol] [rasmolscript] [script source]     - Domain d1ddjc_, region C [Jmol] [rasmolscript] [script source]     - Domain d1ddjd_, region D [Jmol] [rasmolscript] [script source] Fold representative 1ddj 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: [1ddj_A] [1ddj_B] [1ddj_C] [1ddj_D] SWISS-PROT database: [P00747] Domain organization of [PLMN_HUMAN] by SWISSPFAM Domain found in 1DDJ: [Tryp_SPc ] by SMART Alignments of the sequence of 1DDJ with the sequences similar proteins can be viewed for 1DDJ's classification [PLMN_HUMAN] 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 [PLMN_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 1DDJ

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

Movements, Movies and Images

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

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