5GDS	Hydrolase Hydrolase Inhibitor	date	Jul 17, 1997
title	Hirunorms Are True Hirudin Mimetics. The Crystal Structure O Alpha-Thrombin:Hirunorm V Complex
authors	G.De Simone, A.Lombardi, S.Galdiero, F.Nastri, R.Della Morte, N.S C.Pedone, M.Bolognesi, V.Pavone
compound		source
Molecule: Alpha-Thrombin Chain: L Ec: 3.4.21.5		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Organ: Blood Tissue: Plasma
Molecule: Alpha-Thrombin Chain: H Ec: 3.4.21.5		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Organ: Blood Tissue: Plasma
Molecule: Hirunorm V Chain: I Engineered: Yes
symmetry	Space Group: C 1 2 1	R_factor 0.176 R_Free NULL
crystal cell	length a length b length c angle alpha angle beta angle gamma 71.900 72.800 73.300 90.00 100.70 90.00
method	X-Ray Diffraction	resolution	2.10 Å
ligand	AIB, ALC, CHG, DGL, NAG, NAL	enzyme	Hydrolase E.C.3.4.21.5 BRENDA
related structures	by homologous chain: 1AIX, 1C4V, 1D3P
Gene Ontology	Chain Function Process Component H L
Primary reference	Hirunorms are true hirudin mimetics. The crystal structure of human alpha-thrombin-hirunorm V complex., De Simone G, Lombardi A, Galdiero S, Nastri F, Della Morte R, Staiano N, Pedone C, Bolognesi M, Pavone V, Protein Sci 1998 Feb;7(2):243-53. PMID:9521099

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (61 Kb) [Save to disk] Biological Unit Coordinates (5gds.pdb1.gz) 54 Kb LPC: Ligand-Protein Contacts for 5GDS CSU: Contacts of Structural Units for 5GDS Likely Quarternary Molecular Structure file(s) for 5GDS Structure Factors (156 Kb) Retrieve 5GDS in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5GDS from S2C, [Save to disk] Re-refined 5gds structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5GDS 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 5GDS

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 5GDS, from MSDmotif at EBI Genome occurence of 5GDS's fold from GeneCensus Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d5gds.1, region L:,H [Jmol] [rasmolscript] [script source] 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: [5gds] [5gds_H] [5gds_L] [5gds_I] SWISS-PROT database: [P00734] Domain organization of [THRB_HUMAN] by SWISSPFAM Domain found in 5GDS: [Tryp_SPc ] by SMART

Other resources with information on 5GDS

Community annotation for 5GDS at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Domain movements in 5GDS from the Database of Macromolecular Movements. Images from IMB Jena Image Library of Biological Macromolecules.

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