1D3D	Hydrolase Hydrolase Inhibitor	date	Sep 29, 1999
title	Crystal Structure Of Human Alpha Thrombin In Complex With Benzothiophene Inhibitor 4
authors	N.Y.Chirgadze
compound		source
Molecule: Alpha-Thrombin Chain: A Ec: 3.4.21.5		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Organ: Blood
Molecule: Alpha-Thrombin Chain: B Ec: 3.4.21.5		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Organ: Blood
Molecule: Hirugen Chain: H		Organism_scientific: Hirudo Medicinalis Organism_common: Medicinal Leech Organism_taxid: 6421
symmetry	Space Group: C 1 2 1	R_factor 0.175 R_Free 0.223
crystal cell	length a length b length c angle alpha angle beta angle gamma 71.110 71.888 73.321 90.00 100.60 90.00
method	X-Ray Diffraction	resolution	2.04 Å
ligand	BZT, NA, NAG, TYS BindingDB	enzyme	Hydrolase E.C.3.4.21.5 BRENDA
related structures	by homologous chain: 1RIW, 1WAY
Gene Ontology	Chain Function Process Component A B
Primary reference	The crystal structures of human alpha-thrombin complexed with active site-directed diamino benzo[b]thiophene derivatives: a binding mode for a structurally novel class of inhibitors., Chirgadze NY, Sall DJ, Briggs SL, Clawson DK, Zhang M, Smith GF, Schevitz RW, Protein Sci 2000 Jan;9(1):29-36. PMID:10739244

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (56 Kb) [Save to disk] Biological Unit Coordinates (1d3d.pdb1.gz) 52 Kb LPC: Ligand-Protein Contacts for 1D3D CSU: Contacts of Structural Units for 1D3D Likely Quarternary Molecular Structure file(s) for 1D3D Retrieve 1D3D in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1D3D from S2C, [Save to disk]

View 1D3D 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 1D3D

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1D3D, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1d3d.1, region A:,B [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: [1d3d] [1d3d_A] [1d3d_B] [1d3d_H] SWISS-PROT database: [P01050] [P00734] Domain organization of [HIRV1_HIRME] [THRB_HUMAN] by SWISSPFAM Domain found in 1D3D: [Tryp_SPc ] by SMART

Other resources with information on 1D3D

Community annotation for 1D3D at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Domain movements in 1D3D from the Database of Macromolecular Movements. Images from IMB Jena Image Library of Biological Macromolecules.

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