1D3T	Hydrolase Hydrolase Inhibitor	date	Sep 30, 1999
title	Crystal Structure Of Human Alpha Thrombin In Complex With Benzo[B]Thiophene Inhibitor 1
authors	N.Y.Chirgadze
compound		source
Molecule: Alpha-Thrombin Chain: A Fragment: Light Chain Ec: 3.4.21.5 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Tissue: Blood
Molecule: Alpha-Thrombin Chain: B Fragment: Heavy Chain Ec: 3.4.21.5 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Tissue: 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 0.172 R_Free 0.235
crystal cell	length a length b length c angle alpha angle beta angle gamma 71.140 71.850 72.960 90.00 100.50 90.00
method	X-Ray Diffraction	resolution	3.00 Å
ligand	BT1, NA, NAG, TYS BindingDB	enzyme	Hydrolase E.C.3.4.21.5 BRENDA
related structures	by homologous chain: 1DWE, 1NRP
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] (50 Kb) [Save to disk] Biological Unit Coordinates (1d3t.pdb1.gz) 45 Kb LPC: Ligand-Protein Contacts for 1D3T CSU: Contacts of Structural Units for 1D3T Likely Quarternary Molecular Structure file(s) for 1D3T Retrieve 1D3T in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1D3T from S2C, [Save to disk]

View 1D3T 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 1D3T

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1D3T, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1d3t.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: [1d3t_B] [1d3t] [1d3t_H] [1d3t_A] SWISS-PROT database: [P01050] [P00734] Domain organization of [HIRV1_HIRME] [THRB_HUMAN] by SWISSPFAM Domain found in 1D3T: [Tryp_SPc ] by SMART

Other resources with information on 1D3T

Community annotation for 1D3T at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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