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 Diffraction	resolution	2.80 Å
ligand	CA, NAG	enzyme
related structures	by homologous chain: 1LTJ, 1RF0
Gene Ontology	Chain Function Process Component E, B eukaryotic cell surface bind... chaperone binding platelet degranulation blood coagulation hemostasis platelet activation response to calcium ion extracellular region fibrinogen complex extracellular space plasma membrane cell cortex external side of plasma memb... platelet alpha granule platelet alpha granule lumen... blood microparticle F, C eukaryotic cell surface bind... metal ion binding platelet degranulation blood coagulation hemostasis platelet activation response to calcium ion extracellular region fibrinogen complex extracellular space plasma membrane cell cortex external side of plasma memb... platelet alpha granule platelet alpha granule lumen... blood microparticle
Primary reference	2.8 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 (489 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 1LT9

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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_A] [1lt9_B] [1lt9_C] [1lt9_D] [1lt9_E] [1lt9_F] 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)

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