1RFI	Hydrolase Dna	date	Nov 10, 2003
title	Crystal Structure Of Human Tyrosyl-Dna Phosphodiesterase Com With Vanadate, Pentapeptide Klnyk, And Tetranucleotide Agtc
authors	D.R.Davies, H.Interthal, J.J.Champoux, W.G.Hol
compound		source
Molecule: 5'-D(Apgptpc)-3' Chain: D, F Engineered: Yes		Synthetic: Yes
Molecule: Tyrosyl-Dna Phosphodiesterase 1 Chain: A, B Fragment: Residues 149-608 Synonym: Tyr-Dna Phosphodiesterase 1, Tdp1 Ec: 3.1.4.- Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Tdp1 Expression_system: Escherichia Coli Bl21 Expression_system_taxid: 511693 Expression_system_strain: Bl21 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet15b
Molecule: Topoisomerase I-Derived Peptide Chain: C, E Fragment: Residues 720-724 Engineered: Yes Mutation: Yes		Synthetic: Yes Other_details: The Peptide Was Chemically Synthesized. The Of The Peptide Is Naturally Found In "Homo Sapiens" (Human)
symmetry	Space Group: P 21 21 21	R_factor 0.188 R_Free 0.227
crystal cell	length a length b length c angle alpha angle beta angle gamma 49.820 104.832 193.539 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.20 Å
ligand	SPM, VO4	enzyme	Hydrolase E.C.3.1.4 BRENDA
related structures	by homologous chain: 1RG1, 1RGU
Gene Ontology	Chain Function Process Component A, B
Primary reference	Explorations of peptide and oligonucleotide binding sites of tyrosyl-DNA phosphodiesterase using vanadate complexes., Davies DR, Interthal H, Champoux JJ, Hol WG, J Med Chem 2004 Feb 12;47(4):829-37. PMID:14761185

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (153 Kb) [Save to disk] Biological Unit Coordinates (1rfi.pdb1.gz) 74 Kb Biological Unit Coordinates (1rfi.pdb2.gz) 73 Kb LPC: Ligand-Protein Contacts for 1RFI CSU: Contacts of Structural Units for 1RFI Likely Quarternary Molecular Structure file(s) for 1RFI Structure Factors (413 Kb) Retrieve 1RFI in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1RFI from S2C, [Save to disk] Re-refined 1rfi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1RFI 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 1RFI

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 1RFI, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1rfia1, region A:162-350 [Jmol] [rasmolscript] [script source]     - Domain d1rfia2, region A:351-608 [Jmol] [rasmolscript] [script source]     - Domain d1rfib1, region B:162-350 [Jmol] [rasmolscript] [script source]     - Domain d1rfib2, region B:351-607 [Jmol] [rasmolscript] [script source]

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1rfi_C] [1rfi_F] [1rfi] [1rfi_D] [1rfi_B] [1rfi_A] [1rfi_E] SWISS-PROT database: [Q9NUW8] Domain organization of [TYDP1_HUMAN] by SWISSPFAM

Other resources with information on 1RFI

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

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