Page of Complex

Each NPIDB entry has its own web page named Page of Complex. This page contains information about the complex.

The information is grouped in several sections:

General information

General information section contains information extracted from PDB file.

  • PDB ID, PDB Header, Data are got from HEADER field of PDB file;
    Title is from TITLE field;
    Experimental method and Resolution are from EXPDTA and REMARK respectively;
    Organism is from ORGANISM_SCIENTIFIC subfield of SOURCE field;
    kind is the type of complex, determined using residues in PDB file presented in ATOM fields. Kind may be dna, rna, or hybrid.
    The image of the complex is created in PyMol using first biounit or first model.

    Downloading PDB file, visualization in Jmol and a link to interaction service are available in this section.

Section Quick Links contains links to this complex in other databases and services, such as PDB, PDBe, SRS, MMDB, Jena, OCA, PDBWiki, CATH, PDBsum, HSSP, PQS, DALI, ProteopediA, BIPA, EDS, etc.

Composition of PDB entry and biounits

The section contains PDB files and information about chains of macromolecules in it. The files are asymmetric unit (PDB entry) and biological unit (Biounits). In case when structure is solved with NMR we cut it on single models and each model is present as Model file. Some structures have features, such as duplication of atoms or two or more variants of the structure posed in one coordinate space, that make it difficult to analyze them by standard tools. We revise those structures and put the information in special files called as "bel files", for example 1qpi.bel1.pdb. Each file is available for downloading and visualizing in Jmol.

We use this files for calculating hydrogen bonds, water bridges, hydrophobic interactions, identification of Pfam domains, etc. However, we use only one file from presented in this section. If structure is solved with NMR method and has a multimodel file, we use the first model only, if the method is X-RAY and the complex has corrected "bel file" we use it, if there is no "bel file", then we use the first biological unit. In consequence this selected file is called the actual unit.

Interaction service is available for the "actual unit". This service allows a user to visualize each individual bond in structure and to download datasets of Hbonds, water bridges, and hydrophobic clusters.

http://npidb.belozersky.msu.ru/img/npidb_help/composition_of_biounits_1.png

Pfam domains

The detection of Pfam domains is done using the HMM profiles downloaded from Pfam server, HMMER3 software and PfamScan tools with E-value threshold of 0.001.

The output of PfamScan is presented in the Pfam domains table, where Nuc. Chains are chains of nucleic acid that have any kind of interaction with the corresponding domain. A user can also download the structure of the Pfam domain with the part of interacting nucleic acid in PDB format or visualize it with Jmol.

SCOP domains

Information on SCOP domains was downloaded from SCOP server and is presented in the SCOP domains table, where Nuc. Chains are chains of nucleic acid that have an interaction with the corresponding domain. A user can also download the structure of the SCOP domain with the part of interacting nucleic acid in PDB format or visualize it with Jmol.

Sequences

In the Sequences section sequences of macromolecules (in the "actual unit") are presented together with information on secondary structure (for proteins) and information of bonds between protein and nucleic acid residues.

Sequences are hidden by default, to visualize a sequence click "SHOW" button:

http://npidb.belozersky.msu.ru/img/npidb_help/sequences.png

The protein chain 'A' is shown on image above, where:

  • Serial number is a serial number of a residue.

  • PDB number is a number of a residue in the PDB file.

  • Sequence is the sequence of the macromolecule (chain A) in one-letter format.

  • Secondary str. is the secondary structure of the macromolecule (for protein chains only!), where

    • H is for alpha helix
      E is for beta strand
      C is for coil
      T is for turn
      G is for 310-helix

  • Residue type is a type of a residue. Grey means protein, orange means deoxyribonucleotide, purple means ribonucleotide

  • Hbonds is a number of hydrogen bonds with nucleic acid (for protein chains) or with protein (for nucleic chains) formed by a residue.

  • Water bridges is a number of water bridges.

  • Hydrophobic clusters is a serial number of a hydrophobic cluster in which a residue is involved.

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