Home . Database of structures of nucleic acid - protein complexes . ... List of complexes . Pfam families . SCOP families . Interaction classes . ... NPIDB . ... Information on SCOP and Pfam domains detected in protein chains is presented. ... Each family has its own web page with the list of entries that include domains of the family. ... List of SCOP domains occurred in DNA-protein and RNA-protein complexes is organized in tree-like form, according to the SCOP classification. ...
... List of complexes . ... NPIDB, Nucleic acid ? Protein Interaction DataBase provides an access to structured and organized information about all available structures of DNA ? ... Since 2003, the database is available online. ... NPIDB: nucleic acid?protein interaction database . ... An updated version of NPIDB includes new classifications of DNA-protein complexes and their families . ... Sergey Vasilyev (the main developer of the first version of the database) . ... 03-04-48476 (2003 2005) . ...
... 5DPK structure . Page of complex: 5DPK . Home Browse Download Help About Us . ... PDB ID . ... MUTY ADENINE GLYCOSYLASE BOUND TO A TRANSITION STATE ANALOG (1N) PAIRED WITH D(8-OXOG) IN DUPLEXED DNA TO 2.2 A . ... View in . ... Protein chains: . DNA chains: . ... 5dpk.pdb1.pdb . ... Pfam domains . ... Download file with secondary structure created by Stride . 5dpk.pdb1.pdb: [ download sequences in FASTA format ] . ... Click "SHOW" for view sequence . ... NPIDB team 2003 - 2016 . ...
... Interaction classes . ... List of Contact Types: . ... Contact with Major Groove of DNA by helices, loops and Minor Groove by any element(s) . ... Contact with Major Groove of DNA by strands, loops and Minor Groove by any element(s) . ... Contact with Major Groove of DNA by loops and Minor Groove by any element(s) . ... Contact with Major Groove of DNA by any element(s) and Minor Groove by helices, loops . ... Contact with Major Groove of DNA by any element(s) and Minor Groove by loops . ...
Home . Interaction classes . Classes of protein-DNA interaction of SCOP families . Home Browse Download Help About Us . ... Pfam families . SCOP families . ... Interaction modes . ... Mj = major groove . Mn = minor groove . ... Interaction class . Number of families . Number of structures . Number of domains . ... 121 . ... 127 . ... NPIDB team 2003 - 2016 . ...
The entry 1FJL contains 3 protein chains: A, B, and C, and 3 DNA chains: D, E, and F. The chains A, B, D, and E describe two variants of the complex, one including nucleotide residues DA1 and DT8 of the chain D and DT1 and DA8 of the chain E; another including residues DT1 and DA8 of the chain D and DA1 and DT8 of the chain E. In the original entry, the residues , e.g, DA1 and DT1 of the ... The model 1 contains all atoms of the chain F except of having the altercode "B". ...
The entry 1QPI contains 1 protein chain: A, and 2 DNA chains: M and N. The length of two DNA chains are identical (15 nucleotide residues), their sequences are similar (differ in 3 positions of 15). ... All atoms of the chain N have alter codes "A", and all atoms of the chain M have alter codes "B". All DNA atoms have occupancy 0.5. ...
... Homeodomain is a DNA-binding domain presented in a number of eukariotic transcription factors that are resposible for regulation of key developmental processes. Homeodomains contain three alpha-helixes forming helix-turn-helix (HTH) topology and a flexible, enriched with basic amino acids N-terminal "hand" (residues 1?9), which changes its conformation during DNA binding. ... Such complexes gain in high specific binding and affinity to DNA. ...
... All contacts alignment . ... Hydrophobic contacts . ... The ETS domain is approximately 85-90 aa DNA-binding domain, that specifically interacts with sequences containing the common core trinucleotide GGA. ... Many of the ETS proteins have been shown to be transcription activators, ETS proteins have been implicated in regulation of gene expression during a variety of biological processes, including growth control, transformation, T-cell activation, and developmental programs in many organisms. ...