1DX5	Hydrolase Hydrolase Inhibitor	date	Dec 20, 1999
title	Crystal Structure Of The Thrombin-Thrombomodulin Complex
authors	P.Fuentes-Prior, Y.Iwanaga, R.Huber, R.Pagila, G.Rumennik, M.Seto J.Morser, D.R.Light, W.Bode
compound		source
Molecule: Thrombin Light Chain Chain: A, B, C, D Synonym: Coagulation Factor II Ec: 3.4.21.5		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Secretion: Blood Plasma Other_details: Purified From Frozen Plasma
Molecule: Thrombomodulin Chain: I, J, K, L Fragment: Egf-Like Domains 4 - 6 Synonym: Tm,Fetomodulin Engineered: Yes Mutation: Yes Other_details: Enzymatically Deglycosylated (Pngase F)		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Tissue: Endothelium Gene: Thbd, Thrm Expression_system: Cricetulus Griseus Expression_system_common: Chinese Hamster Expression_system_taxid: 10029
Molecule: Thrombin Heavy Chain Chain: M, N, O, P Synonym: Coagulation Factor II Ec: 3.4.21.5		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Secretion: Blood Plasma Other_details: Purified From Frozen Plasma
symmetry	Space Group: H 3	R_factor 0.200 R_Free 0.241
crystal cell	length a length b length c angle alpha angle beta angle gamma 214.400 214.400 131.410 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.30 Å
ligand	0GJ, CA, FMT, NA, NAG	enzyme	Hydrolase E.C.3.4.21.5 BRENDA
related structures	by homologous chain: 1BTH, 1SGI
Gene Ontology	Chain Function Process Component A, B, C, D J, K, I, L O, N, P, M
Primary reference	Structural basis for the anticoagulant activity of the thrombin-thrombomodulin complex., Fuentes-Prior P, Iwanaga Y, Huber R, Pagila R, Rumennik G, Seto M, Morser J, Light DR, Bode W, Nature 2000 Mar 30;404(6777):518-25. PMID:10761923

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (291 Kb) [Save to disk] Biological Unit Coordinates (1dx5.pdb1.gz) 75 Kb Biological Unit Coordinates (1dx5.pdb2.gz) 75 Kb Biological Unit Coordinates (1dx5.pdb3.gz) 74 Kb Biological Unit Coordinates (1dx5.pdb4.gz) 74 Kb LPC: Ligand-Protein Contacts for 1DX5 CSU: Contacts of Structural Units for 1DX5 Likely Quarternary Molecular Structure file(s) for 1DX5 Retrieve 1DX5 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1DX5 from S2C, [Save to disk]

View 1DX5 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 1DX5

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1DX5, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1dx5.1, region A:,M [Jmol] [rasmolscript] [script source]     - Domain d1dx5.2, region B:,N [Jmol] [rasmolscript] [script source]     - Domain d1dx5.3, region C:,O [Jmol] [rasmolscript] [script source]     - Domain d1dx5.4, region D:,P [Jmol] [rasmolscript] [script source]     - Domain d1dx5i1, region I:345-387 [Jmol] [rasmolscript] [script source]     - Domain d1dx5i2, region I:388-422 [Jmol] [rasmolscript] [script source]     - Domain d1dx5i3, region I:423-462 [Jmol] [rasmolscript] [script source]     - Domain d1dx5j1, region J:345-387 [Jmol] [rasmolscript] [script source]     - Domain d1dx5j2, region J:388-422 [Jmol] [rasmolscript] [script source]     - Domain d1dx5j3, region J:423-462 [Jmol] [rasmolscript] [script source]     - Domain d1dx5k1, region K:345-387 [Jmol] [rasmolscript] [script source]     - Domain d1dx5k2, region K:388-422 [Jmol] [rasmolscript] [script source]     - Domain d1dx5k3, region K:423-462 [Jmol] [rasmolscript] [script source]     - Domain d1dx5l1, region L:345-387 [Jmol] [rasmolscript] [script source]     - Domain d1dx5l2, region L:388-422 [Jmol] [rasmolscript] [script source]     - Domain d1dx5l3, region L:423-462 [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: [1dx5_C] [1dx5_K] [1dx5_G] [1dx5_D] [1dx5_A] [1dx5_F] [1dx5_E] [1dx5_J] [1dx5_I] [1dx5_N] [1dx5_M] [1dx5_O] [1dx5] [1dx5_B] [1dx5_L] [1dx5_H] [1dx5_P] SWISS-PROT database: [P00734] [P07204] Domain organization of [THRB_HUMAN] [TRBM_HUMAN] by SWISSPFAM Domains found in 1DX5: [EGF] [EGF_like] [Tryp_SPc ] by SMART

Other resources with information on 1DX5

Community annotation for 1DX5 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Domain movements in 1DX5 from the Database of Macromolecular Movements. Images from IMB Jena Image Library of Biological Macromolecules.

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