1L4D Hydrolase Hydrolase Activator date Mar 04, 2002
title Crystal Structure Of Microplasminogen-Streptokinase Alpha Domain Complex
authors N.Wakeham, S.Terzyan, P.Zhai, J.A.Loy, J.Tang, X.C.Zhang
compound source
Molecule: Plasminogen
Chain: A
Fragment: Catalytic Domain, Residues 543-791
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_type: Plasmid
Expression_system_plasmid: Pet11

Molecule: Streptokinase
Chain: B
Fragment: Alpha Domain, Residues 14-147
Engineered: Yes

Organism_scientific: Streptococcus Dysgalactiae Subsp. Equisimilis;
Organism_taxid: 119602
Strain: Subsp. Equisimilis
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11
symmetry Space Group: C 2 2 21
R_factor 0.206 R_Free 0.263
crystal
cell
length a length b length c angle alpha angle beta angle gamma
67.449 94.177 126.822 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand SO4 enzyme Hydrolase E.C.3.4.21.7 BRENDA
related structures by homologous chain: 1BUI, 1L4Z, 1RJX
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceEffects of deletion of streptokinase residues 48-59 on plasminogen activation., Wakeham N, Terzyan S, Zhai P, Loy JA, Tang J, Zhang XC, Protein Eng 2002 Sep;15(9):753-61. PMID:12456874
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (66 Kb) [Save to disk]
  • Biological Unit Coordinates (1l4d.pdb1.gz) 61 Kb
  • Biological Unit Coordinates (1l4d.pdb2.gz) 121 Kb
  • Biological Unit Coordinates (1l4d.pdb3.gz) 62 Kb
  • LPC: Ligand-Protein Contacts for 1L4D
  • CSU: Contacts of Structural Units for 1L4D
  • Likely Quarternary Molecular Structure file(s) for 1L4D
  • Structure Factors (130 Kb)
  • Retrieve 1L4D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1L4D from S2C, [Save to disk]
  • Re-refined 1l4d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1L4D 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 1L4D
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1L4D, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1l4da_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1l4db_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1l4d 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: [1l4d] [1l4d_A] [1l4d_B]
  • SWISS-PROT database: [P00747] [P00779]
  • Domain organization of [PLMN_HUMAN] [STRP_STREQ] by SWISSPFAM
  • Domain found in 1L4D: [Tryp_SPc ] by SMART
  • Alignments of the sequence of 1L4D with the sequences similar proteins can be viewed for 1L4D'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 1L4D
  • Community annotation for 1L4D at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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