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High Throughput Processing of the Structural Information of the Protein Data Bank. Zoltán Szabadka , Vince Grolmusz Department of Computer Science Eötvös University, Budapest. What is wrong with the PDB?. It is not uniform, each author has a different style
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High Throughput Processing of the Structural Information of the Protein Data Bank Zoltán Szabadka, Vince Grolmusz Department of Computer Science Eötvös University, Budapest
What is wrong with the PDB? • It is not uniform, each author has a different style • It is hard to process it automatically • Residue numbering is not always sequential • The chemical symbols of the atoms are often missing • It is not easy to tell how many ligands there are in an entry, chain ids are not used consistently • It is not clearly indicated if a molecule has missing atoms, and which atoms are missing • There is a need for a “front-end” database to the PDB
Flow of data Internet local PDB mirror download and check for updates structural decomposition database of structure and coordinate data SQL query SQL query SQL query statistical information test sets of docking algorithms list of binding sites
What type of molecules are there in a PDB entry? • Protein chains (P) • DNA/RNA chains (N) • Ligands (L) • Metals and other small ions (I) • Water molecules (W)
Information stored in the database • Covalent structure of molecules • List of components of each entry • Coordinate data for each atom • Interactions between molecules
E/R diagram of the databasecovalent structure id id molecule contains atom bond type symbol type id contains monomer num
E/R diagram of the databasecomponent structure id entry contains component molecule id pdbid contains type id interaction atom (x,y,z) length
PDB file formats • PDB format This is the original PDB file format, it contains data records in separate lines, each with fixed length and format, eg. ATOM, HETATM, SEQRES, CONECT, etc. • mmCIF format This is a relational database description language, a file contains data tables called categories. • XML format The same tables are described by XML tags. The file sizes are huge, a file contains more data tags then data.
Structural units of an entry • The basic structural unit of both the PDB and the mmCIF format is the so called monomer. It can be a molecule, a molecule fragment or just an atom. • Each such monomer has an at most three letter long code, called monomer id, eg. ALA for alanine, MG for magnesium ion, ACE for acethyl group, or HOH for water. • A protein chain consists of many amino acid monomers, each having a sequence number that indicates its position within the chain. • Similarly, DNA/RNA chains consist of many nucleic acid monomers. • Metals, small ions, water and most ligands are one monomer having a unique monomer id. • The basic problem is that there are certain ligand molecules that consist of two or more monomers, and this information is not always properly annotated in the PDB entries in either formats.
mmCIF data categories • entity List of molecules in the entry, can be of three types: polymer, non-polymer and water. Each molecule has an entity id. • entity_poly Contains the type of polymer entities, eg. polypeptide(L) • struct_asym List of the components in the asymmetric unit. Each component has an asym id and an entity id. • pdbx_poly_seq_scheme Describes the sequence of monomers in a polymer entity. • pdbx_nonpoly_scheme List of the monomers belonging to the non-polymer entities. • atom_site Coordinate data for atoms, whose positions could be experimentally determined.
Structural decompositionbased on the mmCIF format • First we read the list of components in the asymmetric unit. • For each component, we read its entity type, and for each polymer entity, its polymer type. • Then we read the sequence of monomers for the polymer entities, and the list of monomers belonging to the non-polymer entities. • The structure of monomers if known ‘a priori’ from a file named components.cif, which can be found at RCSB’s web site. • So for each monomer, we have a list of atoms, lacking coordinate information. Now we go through the table atom_site, and for each atom, we find the monomer it belongs to, and fill the coordinates for the atom just found. If an atom of a monomer is not found, it will be marked as missing.
Definition of molecule types • Protein chain:a polymer entity of type “polypeptide(L)”, which is at least 10 monomers long • DNA/RNA chain: a polymer entity, which is at least 5 monomers long and its type is either “polydeoxiribonucleotide”, “polyribonucleotide”, or more then half of its monomers are nucleic acids (A,C,G,I,T,U monomer id) • Ion: there is a predefined list of monomer ids, containing metals and small ions • Water: the monomers of the water entity • Ligand: all monomers, that do not belong to the above categories will form the set of ligand monomers
Ligands and binding sites • We define a graph on the atoms that have coordinate data. It will have two types of edges: • covalent: if the distance of the two atoms is less then 1.25 times the sum of their covalent radii • VdW: if it is not covalent, but the distance of the two atoms is less then the sum of their Van der Waals radii • The graph is built using a 3 dimensional kd-tree in O(n log n) time • We go through the edges: • if an edge of covalent type connects two ligand molecules, then they will be joined together in one new molecule • if an edge connects a ligand to a protein chain, then this intermolecular interaction will be recorded in the protein-ligand interaction table, marking the binding site of this ligand on the protein surface
PDB version: June 6, 2005 • Number of PDB entries: 31,217 • Number of entries processed: 26,445 • Number of protein chains: 59,842 • Number of different sequences: 18,333 • Number of ligands: 53,834 • Number of different ligand molecules: 6,016 • Number of all atoms: 269,237,779 • Number of atoms in protein chains: 240,243,785 • Number of atoms in DNA/RNA chains: 7,709,842 • Number of atoms in ligands and ions: 2,479,339 • Number of atoms in water: 18,804,813
Distribution of elements in ligands and ions The distribution of the organic and the most frequent inorganic elements among the ligands and ions. We found 70 different elements.
Distribution of elements in protein chains There were 17 different elements in the protein chains, the tables show the number of occurrences, and for the non-standard elements, the monomers that contain them.
Distribution of protein monomers The table shows the distribution of the 20 natural amino acids and selenomethionine in the different chains and in all chains. The other non-standard monomers are listed below.
10gs 1 A 2 3 C 4 Protein-Ligand interactions The table above shows the number of protein-ligand interactions, the number of entries they occur in, and the number of different interaction types while more and more con-ditions are met.
Distribution of missing atoms The distribution of the number of missing atoms from protein chains in the PDB entries. Note, that there are relatively few entries, where only a few atoms are missing.
Distribution of missing segments The distribution of the lengths of missing chain segments at the beginning, at the middle and at the end of the chains. The length is measured in amino acids. Note that in the middle of the chain, typically 4-7 amino acids are missing.
