1NOP	Hydrolase Dna	date	Jan 16, 2003
title	Crystal Structure Of Human Tyrosyl-Dna Phosphodiesterase (Td Complex With Vanadate, Dna And A Human Topoisomerase I-Deri Peptide
authors	D.R.Davies, H.Interthal, J.J.Champoux, W.G.J.Hol
compound		source
Molecule: 5'-D(Apgpapgptpt)-3' Chain: D, F Engineered: Yes		Synthetic: Yes Other_details: This Sequence Is Derived From A Sequence Kno A Target For Topoisomerase I;
Molecule: Tyrosyl-Dna Phosphodiesterase 1 Chain: A, B Fragment: Residues 149-608 Synonym: Tdp1 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 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 Fragment: Residues 720-727 Engineered: Yes		Synthetic: Yes Other_details: This Sequence Occurs Naturally In Human Topo I. This Sequence Includes The Catalytic Tyrosine Residue Th Becomes Transiently Covalently Attatched To The 3' End Of D
symmetry	Space Group: P 21 21 21	R_factor 0.206 R_Free 0.252
crystal cell	length a length b length c angle alpha angle beta angle gamma 49.803 104.719 193.924 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.30 Å
ligand	VO4	enzyme
related structures	by homologous chain: 1QZQ, 1RH0
Gene Ontology	Chain Function Process Component A, B
Primary reference	Crystal structure of a transition state mimic for Tdp1 assembled from vanadate, DNA, and a topoisomerase I-derived peptide., Davies DR, Interthal H, Champoux JJ, Hol WG, Chem Biol 2003 Feb;10(2):139-47. PMID:12618186

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (146 Kb) [Save to disk] Biological Unit Coordinates (1nop.pdb1.gz) 72 Kb Biological Unit Coordinates (1nop.pdb2.gz) 71 Kb LPC: Ligand-Protein Contacts for 1NOP CSU: Contacts of Structural Units for 1NOP Likely Quarternary Molecular Structure file(s) for 1NOP Structure Factors (337 Kb) Retrieve 1NOP in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1NOP from S2C, [Save to disk] Re-refined 1nop structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1NOP 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 1NOP

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 1NOP, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1nopa1, region A:162-350 [Jmol] [rasmolscript] [script source]     - Domain d1nopa2, region A:351-608 [Jmol] [rasmolscript] [script source]     - Domain d1nopb1, region B:159-350 [Jmol] [rasmolscript] [script source]     - Domain d1nopb2, region B:351-607 [Jmol] [rasmolscript] [script source]

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1nop] [1nop_A] [1nop_B] [1nop_C] [1nop_F] [1nop_D] SWISS-PROT database: [Q9NUW8] Domain organization of [TYDP1_HUMAN] by SWISSPFAM

Other resources with information on 1NOP

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

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