1K3X	Hydrolase Dna	date	Oct 04, 2001
title	Crystal Structure Of A Trapped Reaction Intermediate Of The Enzyme Endonuclease Viii With Brominated-Dna
authors	G.Golan, D.O.Zharkov, R.Gilboa, A.S.Fernandes, J.H.Kycia, S.E.Ger R.A.Rieger, A.P.Grollman, G.Shoham
compound		source
Molecule: 5'-D(Gpgpcp(Bru)P(Bru)Pcpap(Bru)Pcpcp( Pgpg)-3'; Chain: B Engineered: Yes		Synthetic: Yes
Molecule: 5'-D(Cpcpapgpgpap(Ped)Pgpapapgpcpc)- Chain: C Engineered: Yes		Synthetic: Yes
Molecule: Endonuclease Viii Chain: A Ec: 3.2.2.- Engineered: Yes		Organism_scientific: Escherichia Coli Organism_taxid: 562 Gene: Nei Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid
symmetry	Space Group: P 43 2 2	R_factor R_Free
crystal cell	length a length b length c angle alpha angle beta angle gamma 76.495 76.495 164.310 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.25 Å
ligand	BRU, GOL, PED, SO4, ZN	enzyme	Hydrolase E.C.3.2.2 BRENDA
note	1K3X is a representative structure
related structures	by homologous chain: 1K3W
Gene Ontology	Chain Function Process Component A endonuclease activity
Primary reference	Structural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate., Zharkov DO, Golan G, Gilboa R, Fernandes AS, Gerchman SE, Kycia JH, Rieger RA, Grollman AP, Shoham G, EMBO J 2002 Feb 15;21(4):789-800. PMID:11847126

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (127 Kb) [Save to disk] Biological Unit Coordinates (1k3x.pdb1.gz) 121 Kb LPC: Ligand-Protein Contacts for 1K3X CSU: Contacts of Structural Units for 1K3X Likely Quarternary Molecular Structure file(s) for 1K3X Retrieve 1K3X in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1K3X from S2C, [Save to disk]

View 1K3X 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 1K3X

Ramachandran plot from PDBSum

Structure-derived information

Conformational Epitope Prediction for 1K3X 1K3XA 1K3XB 1K3XC from the CEP Server. Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1K3X, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1k3xa2, region A:1-124 [Jmol] [rasmolscript] [script source]     - Domain d1k3xa1, region A:125-213 [Jmol] [rasmolscript] [script source]     - Domain d1k3xa3, region A:223-262 [Jmol] [rasmolscript] [script source]

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1k3x] [1k3x_C] [1k3x_B] [1k3x_A] SWISS-PROT database: [P50465] Domain organization of [END8_ECOLI] by SWISSPFAM Domains found in 1K3X: [Fapy_DNA_glyco] [H2TH ] by SMART

Other resources with information on 1K3X

Community annotation for 1K3X at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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