1LT9 Blood Clotting date May 20, 2002
title Crystal Structure Of Recombinant Human Fibrinogen Fragment D
authors M.S.Kostelansky, L.Betts, O.V.Gorkun, S.T.Lord
compound source
Molecule: Fibrinogen Alphaalpha-E Chain
Chain: A, D
Fragment: Fragment D (Residues 126-191)
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_cell_line: Cho Cells

Molecule: Fibrinogen Beta Chain
Chain: B, E
Fragment: Fragment D (Residues 149-461)
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_cell_line: Cho Cells

Molecule: Fibrinogen Gamma Chain
Chain: C, F
Fragment: Fragment D (Residues 96-406)
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_cell_line: Cho Cells
symmetry Space Group: P 21 21 21
R_factor 0.224 R_Free 0.271
crystal
cell
length a length b length c angle alpha angle beta angle gamma
88.727 94.511 227.111 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand CA, NAG enzyme
related structures by homologous chain: 1LTJ, 1RF0
Primary reference2.8 A crystal structures of recombinant fibrinogen fragment D with and without two peptide ligands: GHRP binding to the "b" site disrupts its nearby calcium-binding site., Kostelansky MS, Betts L, Gorkun OV, Lord ST, Biochemistry 2002 Oct 8;41(40):12124-32. PMID:12356313
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (222 Kb) [Save to disk]
  • Biological Unit Coordinates (1lt9.pdb1.gz) 111 Kb
  • Biological Unit Coordinates (1lt9.pdb2.gz) 108 Kb
  • LPC: Ligand-Protein Contacts for 1LT9
  • CSU: Contacts of Structural Units for 1LT9
  • Likely Quarternary Molecular Structure file(s) for 1LT9
  • Structure Factors (536 Kb)
  • Retrieve 1LT9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1LT9 from S2C, [Save to disk]
  • Re-refined 1lt9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1LT9 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 1LT9
  • 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 1LT9, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1lt9a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1lt9b2, region B:161-199 [Jmol] [rasmolscript] [script source]
        - Domain d1lt9b1, region B:200-458 [Jmol] [rasmolscript] [script source]
        - Domain d1lt9c1, region C:142-394 [Jmol] [rasmolscript] [script source]
        - Domain d1lt9c2, region C:96-141 [Jmol] [rasmolscript] [script source]
        - Domain d1lt9d_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1lt9e2, region E:165-199 [Jmol] [rasmolscript] [script source]
        - Domain d1lt9e1, region E:200-458 [Jmol] [rasmolscript] [script source]
        - Domain d1lt9f2, region F:110-141 [Jmol] [rasmolscript] [script source]
        - Domain d1lt9f1, region F:142-394 [Jmol] [rasmolscript] [script source]
  • Fold representative 1lt9 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: [1lt9_C] [1lt9_B] [1lt9_A] [1lt9_F] [1lt9_D] [1lt9] [1lt9_E]
  • SWISS-PROT database: [P02671] [P02675] [P02679]
  • Domain organization of [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] by SWISSPFAM
  • Domain found in 1LT9: [FBG ] by SMART
  • Alignments of the sequence of 1LT9 with the sequences similar proteins can be viewed for 1LT9's classification [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_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 [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1LT9
  • Community annotation for 1LT9 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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