1DEW	Lyase Dna	date	Nov 15, 1999
title	Crystal Structure Of Human Ape1 Bound To Abasic Dna
authors	C.D.Mol, T.Izumi, S.Mitra, J.A.Tainer
compound		source
Molecule: 5'-D(Gpcpgptpcpcp(3dr)Pcpgpapcpgpap Chain: X, U Engineered: Yes Other_details: Dna Contains Abasic Nucleotide 3dr		Synthetic: Yes
Molecule: 5'-D(Gptpcpgptpcpgpgpgpgpapcpgpc)-3 Chain: Y, V Engineered: Yes		Synthetic: Yes
Molecule: Major Apurinicapyrimidinic Endonuclease Chain: A, B Fragment: Ape1 Synonym: Ape1 Ec: 4.2.99.18 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 1 21 1	R_factor 0.195 R_Free 0.286
crystal cell	length a length b length c angle alpha angle beta angle gamma 71.221 72.249 93.749 90.00 94.29 90.00
method	X-Ray Diffraction	resolution	2.65 Å
ligand	3DR, SO4	enzyme	Lyase E.C.4.2.99.18 BRENDA
related structures	by homologous chain: 1DE8, 1E9N
Gene Ontology	Chain Function Process Component A, B
Primary reference	DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination [corrected], Mol CD, Izumi T, Mitra S, Tainer JA, Nature 2000 Jan 27;403(6768):451-6. PMID:10667800

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (124 Kb) [Save to disk] Biological Unit Coordinates (1dew.pdb1.gz) 61 Kb Biological Unit Coordinates (1dew.pdb2.gz) 60 Kb LPC: Ligand-Protein Contacts for 1DEW CSU: Contacts of Structural Units for 1DEW Likely Quarternary Molecular Structure file(s) for 1DEW Structure Factors (221 Kb) Retrieve 1DEW in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1DEW from S2C, [Save to disk] Re-refined 1dew structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1DEW 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 1DEW

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 1DEW, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1dewa_, region A [Jmol] [rasmolscript] [script source]     - Domain d1dewb_, 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: [1dew] [1dew_U] [1dew_X] [1dew_A] [1dew_V] [1dew_B] [1dew_Y] SWISS-PROT database: [P27695] Domain organization of [APEX1_HUMAN] by SWISSPFAM

Other resources with information on 1DEW

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

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