2FFD	Blood Clotting	date	Dec 19, 2005
title	Fibrinogen Fragment D With "A" Knob Peptide Mimic Gprvve
authors	L.Betts
compound		source
Molecule: Fibrinogen Alphaalpha-E Chain Chain: A, D Fragment: Residues 145-210 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Fga Expression_system: Cricetulus Griseus Expression_system_common: Chinese Hamster Expression_system_taxid: 10029 Expression_system_cell_line: Ovary Cells
Molecule: Fibrinogen Beta Chain Chain: B, E Fragment: Residues 179-491 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Fgb Expression_system: Cricetulus Griseus Expression_system_common: Chinese Hamster Expression_system_taxid: 10029 Expression_system_cell_line: Ovary Cells
Molecule: Fibrinogen Gamma Chain Chain: C, F Fragment: Residues 122-432 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Fgg Expression_system: Cricetulus Griseus Expression_system_common: Chinese Hamster Expression_system_taxid: 10029 Expression_system_cell_line: Ovary Cells
Molecule: Gly-Pro-Arg-Val-Val-Glu Peptide Chain: G, H, I, J Engineered: Yes		Synthetic: Yes Other_details: Synthetic Construct
symmetry	Space Group: P 21 21 21	R_factor 0.211 R_Free 0.268
crystal cell	length a length b length c angle alpha angle beta angle gamma 89.521 94.652 227.490 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.89 Å
ligand	CA, FUC, NAG	enzyme
Gene Ontology	Chain Function Process Component A, D E, B F, C
Primary reference	The structure of fibrinogen fragment D with the 'A' knob peptide GPRVVE., Betts L, Merenbloom BK, Lord ST, J Thromb Haemost. 2006 May;4(5):1139-41. PMID:16689770

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (221 Kb) [Save to disk] Biological Unit Coordinates (2ffd.pdb1.gz) 111 Kb Biological Unit Coordinates (2ffd.pdb2.gz) 108 Kb LPC: Ligand-Protein Contacts for 2FFD CSU: Contacts of Structural Units for 2FFD Likely Quarternary Molecular Structure file(s) for 2FFD Structure Factors (335 Kb) Retrieve 2FFD in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2FFD from S2C, [Save to disk] Re-refined 2ffd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2FFD 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 2FFD

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 3D motif for 2FFD, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2ffd_J] [2ffd_C] [2ffd_E] [2ffd_H] [2ffd_G] [2ffd_D] [2ffd_B] [2ffd_F] [2ffd] [2ffd_I] [2ffd_A] SWISS-PROT database: [P02671] [P02675] [P02679] Domain organization of [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] by SWISSPFAM Domain found in 2FFD: [FBG ] by SMART

Other resources with information on 2FFD

Community annotation for 2FFD at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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Images from IMB Jena Image Library of Biological Macromolecules.

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