1DE9	Lyase Dna	date	Nov 13, 1999
title	Human Ape1 Endonuclease With Bound Abasic Dna And Mn2+ Ion
authors	C.D.Mol, T.Izumi, S.Mitra, J.A.Tainer
compound		source
Molecule: 5'-D(Cptpapc)-3' Chain: X, U Engineered: Yes		Synthetic: Yes
Molecule: 5'-D(P(3dr)Pgpaptpc)-3' Chain: Y, V Engineered: Yes		Synthetic: Yes
Molecule: 5'-D(Gpaptpcpgpgptpapg)-3' Chain: Z, W 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 21 21 21	R_factor 0.183 R_Free 0.274
crystal cell	length a length b length c angle alpha angle beta angle gamma 90.060 98.350 101.050 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.00 Å
ligand	3DR, MN	enzyme	Lyase E.C.4.2.99.18 BRENDA
related structures	by homologous chain: 1DE8
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] (106 Kb) [Save to disk] Biological Unit Coordinates (1de9.pdb1.gz) 52 Kb Biological Unit Coordinates (1de9.pdb2.gz) 52 Kb LPC: Ligand-Protein Contacts for 1DE9 CSU: Contacts of Structural Units for 1DE9 Likely Quarternary Molecular Structure file(s) for 1DE9 Structure Factors (149 Kb) Retrieve 1DE9 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1DE9 from S2C, [Save to disk] Re-refined 1de9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1DE9 in 3D

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Visual 3D analysis of 1DE9

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 1DE9, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1de9a_, region A [Jmol] [rasmolscript] [script source]     - Domain d1de9b_, 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: [1de9_B] [1de9_U] [1de9_Z] [1de9_V] [1de9_A] [1de9_X] [1de9] [1de9_Y] [1de9_W] SWISS-PROT database: [P27695] Domain organization of [APEX1_HUMAN] by SWISSPFAM

Other resources with information on 1DE9

Community annotation for 1DE9 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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