Database Accession: DI3010002
Name: Alpha-chain of human fibrinogen bound to bovine epsilon-thrombin
PDB ID: 1bbr
Experimental method: X-ray (2.30 Å)
Source organism: Homo sapiens / Bos taurus
Proof of disorder:
Primary publication of the structure:
Martin PD, Robertson W, Turk D, Huber R, Bode W, Edwards BF
The structure of residues 7-16 of the A alpha-chain of human fibrinogen bound to bovine thrombin at 2.3-A resolution.
(1992) J. Biol. Chem. 267: 7911-20
PMID: 1560020
Abstract:
The tetradecapeptide Ac-D-F-L-A-E-G-G-G-V-R-G-P-R-V-OMe, which mimics residues 7f-20f of the A alpha-chain of human fibrinogen, has been co-crystallized with bovine thrombin from ammonium sulfate solutions in space group P2(1) with unit cell dimensions of a = 83.0 A, b = 89.4 A, c = 99.3 A, and beta = 106.6 degrees. Three crystallographically independent complexes were located in the asymmetric unit by molecular replacement using the native bovine thrombin structure as a model. The standard crystallographic R-factor is 0.167 at 2.3-A resolution. Excellent electron density could be traced for the decapeptide, beginning with Asp-7f and ending with Arg-16f in the active site of thrombin; the remaining 4 residues, which have been cleaved from the tetradecapeptide at the Arg-16f/Gly-17f bond, are not seen. Residues 7f-11f at the NH2 terminus of the peptide form a single turn of alpha-helix that is connected by Gly-12f, which has a positive phi angle, to an extended chain containing residues 13f-16f. The major specific interactions between the peptide and thrombin are 1) a hydrophobic cage formed by residues Tyr-60A, Trp-60D, Leu-99, Ile-174, Trp-215, Leu-9f, Gly-13f, and Val-15f that surrounds Phe-8f; 2) a hydrogen bond linking Phe-8f NH to Lys-97 O;3) a salt link between Glu-11f and Arg-173; 4) two antiparallel beta-sheet hydrogen bonds between Gly-14f and Gly-216; and 5) the insertion of Arg-16f into the specificity pocket. Binding of the peptide is accompanied by a considerable shift in two of the loops near the active site relative to human D-phenyl-L-prolyl-L-arginyl chloromethyl ketone (PPACK)-thrombin.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
metal ion binding Interacting selectively and non-covalently with any metal ion.
Biological process:
positive regulation of protein phosphorylation Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
proteolysis The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
regulation of cell morphogenesis Any process that modulates the frequency, rate or extent of cell morphogenesis. Cell morphogenesis is the developmental process in which the shape of a cell is generated and organized.
positive regulation of intracellular signal transduction Any process that activates or increases the frequency, rate or extent of intracellular signal transduction.
positive regulation of multicellular organismal process Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs.
negative regulation of protein metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of chemical reactions and pathways involving a protein.
regulation of cell development Any process that modulates the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.
humoral immune response An immune response mediated through a body fluid.
defense response to bacterium Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
regulation of defense response Any process that modulates the frequency, rate or extent of a defense response.
regulation of protein localization Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location.
Cellular component:
external side of plasma membrane The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
Structural annotations of the participating protein chains.Entry contents: 4 distinct polypeptide molecules
Chains: F, E, H, L
Notes: Chains F, J, K, G, M, N and I were removed as chains E, F, H and L highlight the biologically relevant interaction.
Name: Fibrinogen alpha chain
Source organism: Homo sapiens
Length: 11 residues
Sequence:Sequence according to PDB SEQRESGDFLAEGGGVR
UniProtKB AC: P02671 (positions: 25-35) Coverage: 1.3%
UniRef90 AC: UniRef90_P02671 (positions: 26-35)
Name: Prothrombin
Source organism: Bos taurus
Length: 109 residues
Sequence:Sequence according to PDB SEQRESSVAEVQPSVLQVVNLPLVERPVCKASTRIRITDNMFCAGYKPGEGKRGDACEGDSGGPFVMKSPYNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDRLGS
UniProtKB AC: P00735 (positions: 517-625) Coverage: 17.4%
UniRef90 AC: UniRef90_P00735 (positions: 517-625)
Name: Prothrombin
Source organism: Bos taurus
Length: 150 residues
Sequence:Sequence according to PDB SEQRESIVEGQDAEVGLSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTVDDLLVRIGKHSRTRYERKVEKISMLDKIYIHPRYNWKENLDRDIALLKLKRPIELSDYIHPVCLPDKQTAAKLLHAGFKGRVTGWGNRRETWTT
UniProtKB AC: P00735 (positions: 367-516) Coverage: 24%
UniRef90 AC: UniRef90_P00735 (positions: 367-516)
Name: Prothrombin
Source organism: Bos taurus
Length: 49 residues
Sequence:Sequence according to PDB SEQRESTSEDHFQPFFNEKTFGAGEADCGLRPLFEKKQVQDQTEKELFESYIEGR
UniProtKB AC: P00735 (positions: 318-366) Coverage: 7.8%
UniRef90 AC: UniRef90_P00735 (positions: 318-366)
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Chain F:
The interacting region of the protein has been shown to be highly flexible corresponding to missing coordinates in X-ray structure (PDB ID: 3h32).
Chain E:
Thrombin consists of a large and a small subunit. Trypsin domain of the large subunit involved in the interaction is known to adopt a stable structure in isolation (see Pfam domain PF00089). A solved structure of a homologous thrombin domain is represented by PDB ID 3pmb.
Chain H:
Thrombin consists of a large and a small subunit. Trypsin domain of the large subunit involved in the interaction is known to adopt a stable structure in isolation (see Pfam domain PF00089). A solved structure of a homologous thrombin domain is represented by PDB ID 3pmb.
Chain L:
Thrombin consists of a large and a small subunit. Trypsin domain of the large subunit involved in the interaction is known to adopt a stable structure in isolation (see Pfam domain PF00089). A solved structure of a homologous thrombin domain is represented by PDB ID 3pmb.
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). The structure can be rotated by left click and hold anywhere on the structure. Representation options can be edited by right clicking on the structure window.
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