2HLO Blood Clotting date Jul 08, 2006
title Crystal Structure Of Fragment D-Dimer From Human Fibrin Comp Gly-Hydroxypro-Arg-Pro-Amide
authors R.F.Doolittle, J.M.Kollman, A.Chen, L.Pandi
compound source
Molecule: Fibrin Alpha Chain
Chain: A, D
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Fibrin Beta Chain
Chain: B, E

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Fibrin, Gamma Polypeptide
Chain: C, F

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Gly-Hyp-Arg-Pro-Amide Peptide Ligand
Chain: G, H
Engineered: Yes

Synthetic: Yes
Other_details: The Peptide Was Chemically Synthesized.
symmetry Space Group: P 21 21 21
R_factor 0.210 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.690 149.480 232.930 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand CA, HYP, NAG, NDG, NH2 enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (228 Kb) [Save to disk]
  • Biological Unit Coordinates (2hlo.pdb1.gz) 115 Kb
  • Biological Unit Coordinates (2hlo.pdb2.gz) 110 Kb
  • LPC: Ligand-Protein Contacts for 2HLO
  • CSU: Contacts of Structural Units for 2HLO
  • Likely Quarternary Molecular Structure file(s) for 2HLO
  • Structure Factors (448 Kb)
  • Retrieve 2HLO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2HLO from S2C, [Save to disk]
  • Re-refined 2hlo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2HLO 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 2HLO
  • 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 2HLO, from MSDmotif at EBI
  • Fold representative 2hlo from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2hlo] [2hlo_C] [2hlo_E] [2hlo_F] [2hlo_A] [2hlo_G] [2hlo_B] [2hlo_H] [2hlo_D]
  • SWISS-PROT database: [P02671] [P02675] [P02679]
  • Domain organization of [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] by SWISSPFAM
  • Domain found in 2HLO: [FBG ] by SMART
  • Alignments of the sequence of 2HLO with the sequences similar proteins can be viewed for 2HLO'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 2HLO
  • Community annotation for 2HLO 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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