1DE8	Lyase Dna	date	Nov 13, 1999
title	Human Apurinicapyrimidinic Endonuclease-1 (Ape1) Bound To A
authors	C.D.Mol, T.Izumi, S.Mitra, J.A.Tainer
compound		source
Molecule: Dna (5'-D(Gpcptpapcp(3dr)Pgpaptpcpg)-3 Chain: X, U Engineered: Yes		Synthetic: Yes
Molecule: Dna (5'-D(Cpgpaptpcpgpgptpapgpc)-3') Chain: Y, V Engineered: Yes		Synthetic: Yes
Molecule: Major Apurinicapyrimidinic Endonuclease Chain: B, A 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: I 41	R_factor 0.190 R_Free 0.312
crystal cell	length a length b length c angle alpha angle beta angle gamma 122.850 122.850 107.070 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.95 Å
ligand	3DR	enzyme	Lyase E.C.4.2.99.18 BRENDA
related structures	by homologous chain: 1DE9, 1DEW
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] (111 Kb) [Save to disk] Biological Unit Coordinates (1de8.pdb1.gz) 54 Kb Biological Unit Coordinates (1de8.pdb2.gz) 54 Kb LPC: Ligand-Protein Contacts for 1DE8 CSU: Contacts of Structural Units for 1DE8 Likely Quarternary Molecular Structure file(s) for 1DE8 Retrieve 1DE8 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1DE8 from S2C, [Save to disk]

View 1DE8 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 1DE8

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1DE8, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1de8a_, region A [Jmol] [rasmolscript] [script source]     - Domain d1de8b_, 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: [1de8_X] [1de8_Y] [1de8_B] [1de8_V] [1de8] [1de8_U] [1de8_A] SWISS-PROT database: [P27695] Domain organization of [APEX1_HUMAN] by SWISSPFAM

Other resources with information on 1DE8

Community annotation for 1DE8 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---