1UCY	Complex (Serine Protease Coagulation)	date	Aug 30, 1996
title	Thrombin Complexed With Fibrinopeptide A Alpha (Residues 7-1 Complexes, One With Epsilon-Thrombin And Two With Alpha-Thr
authors	P.Martin, B.Edwards
compound		source
Molecule: Thrombin Chain: L, J, M Ec: 3.4.21.5 Other_details: Chymotrypsinogen Numbering (Rather Than Sequ System Is Used, Based On The Topological Alignment With The Of Chymotrypsinogen (H.Brandstetter Et Al., 1992, J.Mol.Bio 226, 1085). The N-Terminus Of The Fibrinopeptide Is Acetyla Fibrinopeptide Sequence Numbers Are Ace 6 To Arg 19. A New Opr, Has Been Defined For The Arggly Combination In Which Nitrogen Has Been Replaced With A Ch2, Making The Normal Am Between These Two Residues A Ketone Bond. The Fibrinopeptid Numbering Is Consequently Incremented By 1 After This Resid Keeping With The Fibrinogen Numbering Scheme. There Are Alt Conformations For Residues Pro 18 And Arg 19 In Fibrinopept		Organism_scientific: Bos Taurus Organism_common: Cattle Organism_taxid: 9913 Tissue: Blood
Molecule: Thrombin Chain: H Ec: 3.4.21.5 Other_details: Chymotrypsinogen Numbering (Rather Than Sequ System Is Used, Based On The Topological Alignment With The Of Chymotrypsinogen (H.Brandstetter Et Al., 1992, J.Mol.Bio 226, 1085). The N-Terminus Of The Fibrinopeptide Is Acetyla Fibrinopeptide Sequence Numbers Are Ace 6 To Arg 19. A New Opr, Has Been Defined For The Arggly Combination In Which Nitrogen Has Been Replaced With A Ch2, Making The Normal Am Between These Two Residues A Ketone Bond. The Fibrinopeptid Numbering Is Consequently Incremented By 1 After This Resid Keeping With The Fibrinogen Numbering Scheme. There Are Alt Conformations For Residues Pro 18 And Arg 19 In Fibrinopept		Organism_scientific: Bos Taurus Organism_common: Cattle Organism_taxid: 9913 Tissue: Blood
Molecule: Thrombin Chain: E Ec: 3.4.21.5 Other_details: Chymotrypsinogen Numbering (Rather Than Sequ System Is Used, Based On The Topological Alignment With The Of Chymotrypsinogen (H.Brandstetter Et Al., 1992, J.Mol.Bio 226, 1085). The N-Terminus Of The Fibrinopeptide Is Acetyla Fibrinopeptide Sequence Numbers Are Ace 6 To Arg 19. A New Opr, Has Been Defined For The Arggly Combination In Which Nitrogen Has Been Replaced With A Ch2, Making The Normal Am Between These Two Residues A Ketone Bond. The Fibrinopeptid Numbering Is Consequently Incremented By 1 After This Resid Keeping With The Fibrinogen Numbering Scheme. There Are Alt Conformations For Residues Pro 18 And Arg 19 In Fibrinopept		Organism_scientific: Bos Taurus Organism_common: Cattle Organism_taxid: 9913 Tissue: Blood
Molecule: Fibrinopeptide A-Alpha Chain: F, G, I Fragment: Residues 7 - 19 Engineered: Yes Other_details: Three Complexes Are Presented, One With Epsi Thrombin And Two With Alpha-Thrombin;
Molecule: Thrombin Chain: K, N Ec: 3.4.21.5		Organism_scientific: Bos Taurus Organism_common: Cattle Organism_taxid: 9913 Tissue: Blood
symmetry	Space Group: P 1 21 1	R_factor 0.171 R_Free NULL
crystal cell	length a length b length c angle alpha angle beta angle gamma 82.470 88.780 98.550 90.00 106.21 90.00
method	X-Ray Diffraction	resolution	2.20 Å
ligand	ACE, OPR	enzyme	Hydrolase E.C.3.4.21.5 BRENDA
related structures	by homologous chain: 1ETR, 1WBG
Gene Ontology	Chain Function Process Component E H, N, K J, M, L
Primary reference	Bovine thrombin complexed with an uncleavable analog of residues 7-19 of fibrinogen A alpha: geometry of the catalytic triad and interactions of the P1', P2', and P3' substrate residues., Martin PD, Malkowski MG, DiMaio J, Konishi Y, Ni F, Edwards BF, Biochemistry 1996 Oct 8;35(40):13030-9. PMID:8855938

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (170 Kb) [Save to disk] Biological Unit Coordinates (1ucy.pdb1.gz) 56 Kb Biological Unit Coordinates (1ucy.pdb2.gz) 57 Kb Biological Unit Coordinates (1ucy.pdb3.gz) 57 Kb LPC: Ligand-Protein Contacts for 1UCY CSU: Contacts of Structural Units for 1UCY Likely Quarternary Molecular Structure file(s) for 1UCY Structure Factors (657 Kb) Retrieve 1UCY in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1UCY from S2C, [Save to disk] Re-refined 1ucy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1UCY 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 1UCY

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 1UCY, from MSDmotif at EBI Genome occurence of 1UCY's fold from GeneCensus Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1ucy.2, region J:,K [Jmol] [rasmolscript] [script source]     - Domain d1ucy.1, region L:,H:,E [Jmol] [rasmolscript] [script source]     - Domain d1ucy.3, region M:,N [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: [1ucy_N] [1ucy_I] [1ucy_J] [1ucy] [1ucy_E] [1ucy_M] [1ucy_K] [1ucy_F] [1ucy_G] [1ucy_L] [1ucy_H] SWISS-PROT database: [P00735] Domain organization of [THRB_BOVIN] by SWISSPFAM Domain found in 1UCY: [Tryp_SPc ] by SMART

Other resources with information on 1UCY

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

Movements, Movies and Images

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

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