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 Diffractionresolution 2.00 Å
ligand
enzyme Hydrolase E.C.3.4.21.7 BRENDA
related structures by homologous chain: 1QRZ
Primary referenceHuman 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.
  • 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_C] [1ddj] [1ddj_B] [1ddj_A] [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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