1D9D	Transferase Dna, Rna	date	Oct 27, 1999
title	Crystall Structure Of The Complex Of Dna Polymerase I Klenow With Short Dna Fragment Carrying 2'-0-Aminopropyl-Rna Modif 5'-D(Tcg)-Ap(Auc)-3'
authors	M.Teplova, S.T.Wallace, V.Tereshko, G.Minasov, A.M.Simons, P.D.Co M.Manoharan, M.Egli
compound		source
Molecule: 5'-D(Tpcpgp)-R(Ap(U31)P(C31))-3' Chain: B Engineered: Yes Other_details: 3'-Terminal Adenosine, Uracil, And Cytosine Nucleotides Have 3-Aminopropyl Bound To O2;		Synthetic: Yes
Molecule: Dna Polymerase I Chain: A Fragment: Klenow Fragment Synonym: Pol I, Dna Directed Dna Polymerase Ec: 2.7.7.7 Engineered: Yes		Organism_scientific: Escherichia Coli Organism_taxid: 562 Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 43	R_factor 0.215 R_Free 0.238
crystal cell	length a length b length c angle alpha angle beta angle gamma 102.550 102.550 86.280 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.18 Å
ligand	C31, MG, SO4, U31, ZN	enzyme	Transferase E.C.2.7.7.7 BRENDA
related structures	by homologous chain: 1KFS, 1KRP
Gene Ontology	Chain Function Process Component A
Primary reference	Structural origins of the exonuclease resistance of a zwitterionic RNA., Teplova M, Wallace ST, Tereshko V, Minasov G, Symons AM, Cook PD, Manoharan M, Egli M, Proc Natl Acad Sci U S A 1999 Dec 7;96(25):14240-5. PMID:10588690

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (109 Kb) [Save to disk] Biological Unit Coordinates (1d9d.pdb1.gz) 103 Kb LPC: Ligand-Protein Contacts for 1D9D CSU: Contacts of Structural Units for 1D9D Likely Quarternary Molecular Structure file(s) for 1D9D Structure Factors (364 Kb) Retrieve 1D9D in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1D9D from S2C, [Save to disk] Re-refined 1d9d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1D9D 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 1D9D

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1D9D, from MSDmotif at EBI Structure summary from SCOR (Structural Classification of RNA) Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1d9da1, region A:324-518 [Jmol] [rasmolscript] [script source]     - Domain d1d9da2, region A:519-928 [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: [1d9d_B] [1d9d] [1d9d_A] SWISS-PROT database: [P00582] Domain organization of [DPO1_ECOLI] by SWISSPFAM Domains found in 1D9D: [35EXOc] [POLAc ] by SMART

Other resources with information on 1D9D

Community annotation for 1D9D at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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