PDB: Protein Data Bank

1
PDB Protein Data Bank

• Research Collaboratory for Structure
  Bioinformatics (RCSB)

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Outline

• Introduction
• 20 Amino Acid Structure
• Example for Information of PDB File
• Related Papers

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Introduction

• The PDB was established in 1971
• The single worldwide repository for the
  processing and distribution of 3-D biological
  macromolecular structure data
• 19225 Structures 19 Nov, 2002
• What is PDB?

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Statistics List
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20 Amino Acid - 1
Source http//prowl.rockefeller.edu/aainfo/struct
.htm

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20 Amino Acid - 2
Source http//prowl.rockefeller.edu/aainfo/struct
.htm
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20 Amino Acid - 3
Source http//prowl.rockefeller.edu/aainfo/struct
.htm
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Three-dimensional Structure of Myoglobin
Source Lectures of BioInfo by yukijuan
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Distribution of Amino Acids in Myoglobin
Hydrophobic amino acids Charged amino acids
others
Source Lectures of BioInfo by yukijuan
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PDB File Format

• Example 4HHB
• Tag Explanation
• SEQRES
• MODRES
• HETNAM
• ATOM
• SIGATM
• TER
• HETATM
• SHEET
• TURN

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Tag Explanation

• SEQRES
• SEQRES records contain the amino acid or nucleic
  acid sequence of residues in each chain of the
  macromolecule that was studied.
• MODRES
• The MODRES record provides descriptions of
  modifications (e.g., chemical or
  post-translational) to protein and nucleic acid
  residues.
• HETNAM
• This record gives the chemical name of the
  compound with the given hetID.
• ATOM
• The ATOM records present the atomic coordinates
  for standard residues.

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• SIGATM
• The SIGATM records present the standard deviation
  of atomic parameters as they appear in ATOM and
  HETATM records.
• TER
• The TER record indicates the end of a list of
  ATOM/HETATM records for a chain.
• HETATM
• The HETATM records present the atomic coordinate
  records for atoms within "non-standard" groups.
• SHEET
• SHEET records are used to identify the position
  of sheets in the molecule.
• TRUN
• The TURN records identify turns and other short
  loop turns which normally connect other secondary
  structure segments

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Summary Information for 4HHB
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Related Papers

• A New Algorithm For The Alignment Of Multiple
  Protein Structures Using Monte Carlo
  Optimization, Guda C, Scheeff ED, Bourne PE,
  Shindyalov IN. , Pac Symp Biocomput, 2001
• Protein structure alignment by incremental
  combinatorial extension (CE) of the optimal path,
  IN Shindyalov, PE Bourne, Protein Engineering,
  Vol 11, 739-747, 1998
• A database and tools for 3-D protein structure
  comparison and alignment using the Combinatorial
  Extension (CE) algorithm.Nucleic Acids Res. 2001
  Jan 129(1)228-9.
• Novel computer program for fast exact calculation
  of accessible and molecular surface areas and
  average surface curvature, Oleg V. Tsodikov, M.
  Thomas Record Jr., Yuri V. Sergeev, Journal of
  Computational Chemistry, 2002