1F8Y	Transferase	date	Jul 05, 2000
title	Crystal Structure Analysis Of Nucleoside 2-Deoxyribosyltrans Complexed With 5-Methyl-2'-Deoxypseudouridine
authors	S.R.Armstrong, W.J.Cook, S.A.Short, S.E.Ealick
compound		source
Molecule: Nucleoside 2-Deoxyribosyltransferase Chain: A, B Ec: 2.4.2.6		Organism_scientific: Lactobacillus Leichmannii Organism_taxid: 28039
symmetry	Space Group: I 21 3	R_factor 0.160 R_Free 0.218
crystal cell	length a length b length c angle alpha angle beta angle gamma 149.600 149.600 149.600 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.40 Å
ligand	5MD	enzyme	Transferase E.C.2.4.2.6 BRENDA
note	1F8Y is a representative structure
related structures	by homologous chain: 1F8X
Gene Ontology	Chain Function Process Component A, B
Primary reference	Crystal structures of nucleoside 2-deoxyribosyltransferase in native and ligand-bound forms reveal architecture of the active site., Armstrong SR, Cook WJ, Short SA, Ealick SE, Structure 1996 Jan 15;4(1):97-107. PMID:8805514

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (57 Kb) [Save to disk] Biological Unit Coordinates (1f8y.pdb1.gz) 156 Kb LPC: Ligand-Protein Contacts for 1F8Y CSU: Contacts of Structural Units for 1F8Y Likely Quarternary Molecular Structure file(s) for 1F8Y Retrieve 1F8Y in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1F8Y from S2C, [Save to disk]

View 1F8Y 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 1F8Y

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1F8Y, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1f8ya_, region A [Jmol] [rasmolscript] [script source]     - Domain d1f8yb_, region 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: [1f8y_A] [1f8y_B] [1f8y] SWISS-PROT database: [Q9R5V5] Domain organization of [NTD_LACLE] by SWISSPFAM

Other resources with information on 1F8Y

Community annotation for 1F8Y at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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