2HOD	Blood Clotting Peptide	date	Jul 14, 2006
title	Crystal Structure Of Fragment D From Human Fibrinogen Comple Gly-Hydroxypro-Arg-Pro-Amide
authors	R.F.Doolittle, J.M.Kollman, A.Chen, L.Pandi
compound		source
Molecule: Fibrinogen Alpha Chain Chain: A, D, G, J		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606
Molecule: Fibrinogen Beta Chain Chain: B, E, H, K		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606
Molecule: Fibrinogen, Gamma Polypeptide Chain: C, F, I, L		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606
Molecule: Gly-Hydroxypro-Arg-Pro-Amide Peptide Ligand Chain: M, N, O, P, Q, R, S, T Engineered: Yes		Synthetic: Yes Other_details: The Peptide Was Chemically Synthesized.
symmetry	Space Group: P 1 2 1	R_factor 0.268 R_Free 0.347
crystal cell	length a length b length c angle alpha angle beta angle gamma 81.647 47.069 431.460 90.00 90.06 90.00
method	X-Ray Diffraction	resolution	2.90 Å
ligand	CA, HYP, NAG, NDG, NH2	enzyme
Gene Ontology	Chain Function Process Component F, C, I, L 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 K, E, B, H 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

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (463 Kb) [Save to disk] Biological Unit Coordinates (2hod.pdb1.gz) 120 Kb Biological Unit Coordinates (2hod.pdb2.gz) 118 Kb Biological Unit Coordinates (2hod.pdb3.gz) 120 Kb Biological Unit Coordinates (2hod.pdb4.gz) 120 Kb LPC: Ligand-Protein Contacts for 2HOD CSU: Contacts of Structural Units for 2HOD Likely Quarternary Molecular Structure file(s) for 2HOD Structure Factors (806 Kb) Retrieve 2HOD in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2HOD from S2C, [Save to disk] Re-refined 2hod structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2HOD 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 2HOD

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 2HOD, from MSDmotif at EBI Fold representative 2hod from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2hod_A] [2hod_B] [2hod_C] [2hod_D] [2hod_E] [2hod_F] [2hod_G] [2hod_H] [2hod_I] [2hod_J] [2hod_K] [2hod_L] [2hod_M] [2hod_N] [2hod_O] [2hod_P] [2hod_Q] [2hod_R] [2hod_S] [2hod_T] SWISS-PROT database: [P02671] [P02675] [P02679] Domain organization of [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] by SWISSPFAM Domain found in 2HOD: [FBG ] by SMART Alignments of the sequence of 2HOD with the sequences similar proteins can be viewed for 2HOD'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 2HOD

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

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