1BML	Blood Clotting	date	May 25, 1999
title	Complex Of The Catalytic Domain Of Human Plasmin And Strepto
authors	X.Wang, X.C.Zhang
compound		source
Molecule: Plasmin Chain: A, B Fragment: Catalytic Domain Ec: 3.4.21.7 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Bl21 Expression_system_taxid: 511693 Expression_system_strain: Bl21 Expression_system_vector: Pet11
Molecule: Streptokinase Chain: C, D		Organism_scientific: Streptococcus Dysgalactiae Subsp. Equi Organism_taxid: 119602 Strain: Subsp. Equisimilis
symmetry	Space Group: P 1 21 1	R_factor 0.201 R_Free 0.291
crystal cell	length a length b length c angle alpha angle beta angle gamma 80.030 125.050 86.790 90.00 105.41 90.00
method	X-Ray Diffraction	resolution	2.90 Å
ligand		enzyme	Hydrolase E.C.3.4.21.7 BRENDA
related structures	by homologous chain: 1L4Z
Gene Ontology	Chain Function Process Component A, 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	Crystal structure of the catalytic domain of human plasmin complexed with streptokinase., Wang X, Lin X, Loy JA, Tang J, Zhang XC, Science 1998 Sep 11;281(5383):1662-5. PMID:9733510

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (174 Kb) [Save to disk] Biological Unit Coordinates (1bml.pdb1.gz) 169 Kb Biological Unit Coordinates (1bml.pdb2.gz) 86 Kb Biological Unit Coordinates (1bml.pdb3.gz) 86 Kb CSU: Contacts of Structural Units for 1BML Likely Quarternary Molecular Structure file(s) for 1BML Retrieve 1BML in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1BML from S2C, [Save to disk]

View 1BML 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 1BML

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 1BML, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1bmla_, region A [Jmol] [rasmolscript] [script source]     - Domain d1bmlb_, region B [Jmol] [rasmolscript] [script source]     - Domain d1bmlc1, region C:12-148 [Jmol] [rasmolscript] [script source]     - Domain d1bmlc2, region C:149-284 [Jmol] [rasmolscript] [script source]     - Domain d1bmlc3, region C:285-372 [Jmol] [rasmolscript] [script source]     - Domain d1bmld1, region D:12-148 [Jmol] [rasmolscript] [script source]     - Domain d1bmld2, region D:149-284 [Jmol] [rasmolscript] [script source]     - Domain d1bmld3, region D:285-372 [Jmol] [rasmolscript] [script source] Fold representative 1bml 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: [1bml_A] [1bml_B] [1bml_C] [1bml_D] SWISS-PROT database: [P00747] [P00779] Domain organization of [PLMN_HUMAN] [STRP_STREQ] by SWISSPFAM Domain found in 1BML: [Tryp_SPc ] by SMART Alignments of the sequence of 1BML with the sequences similar proteins can be viewed for 1BML's classification [PLMN_HUMAN] [STRP_STREQ] 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] [STRP_STREQ] at ProtoMap. Click on the Cluster number.

Other resources with information on 1BML

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

Movements, Movies and Images

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

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