The best way to do this will depend on exactly what you want to fetch...

If you want all the chain sequences described in the structure (both protein and nucleotide), then a simple fetch from one of the Worldwide Protein Data Bank (wwPDB) sites will do the job, e.g. to get the sequences for PDB:10MH:

• RCSB: http://pdb.org/pdb/files/fasta.txt?structureIdList=10MH
• PDBj: http://pdbj.org/fasta_seq_data/10mh_seq.txt

Sample Java code for fetching data from a web site can be found with an Internet search. FWIW the site I usually use to remind myself of the method specifics is part of the EMBL-EBI's Web Services tutorials, for example using java.net http://www.ebi.ac.uk/Tools/webservices/tutorials/06_programming/java/rest/java.net

If you want the sequence for a specific chain from a structure, then the EMBL-EBI's dbfetch and WSDbfetch services are an option. These know how to deal with common forms of structure and chain identifiers and the case sensitivity rules for the chain identifier. For details of the supported PDB identifier formats see: http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/dbfetch.databases#pdb. They also support retrieval of all sequences for a structure, and if using the specific database names 'pdbaa' and 'pdbna' retrieval of only the protein or nucleotide sequences for a structure.

In BioJava you can also extract the ATOM and SEQRES chain sequences from the PDB structure, see:

• Generating Sequence From Pdb File Using Biojava
• BioJava:CookBook:
  • BioJava:CookBook:PDB:datamodel
  • BioJava:CookBook:PDB:seqres
  • BioJava:CookBook:PDB:read3.0

i think this code is a demo, it should work with you

   import java.io.BufferedReader;
   import java.io.File;
   import java.io.FileOutputStream;
  import java.io.FileReader;

   import org.biojavax.Namespace;
   import org.biojavax.RichObjectFactory;
   import org.biojavax.bio.seq.RichSequence;
   import org.biojavax.bio.seq.RichSequenceIterator;



public class ReadWriteGES_BJ1_6{

public static void main(String[] args) {
    BufferedReader br = null;
    Namespace ns = null;
            //this path is used for destination file too
    String filePath= "/whereYourFileIs/sequences";
    String insdExt=".gbc";
    String fastaExt=".FASTA";


    try{
        br = new BufferedReader(new FileReader(filePath+insdExt));
        ns = RichObjectFactory.getDefaultNamespace();


             // You can use any of the convenience methods found in the BioJava 1.6 API
                    RichSequenceIterator rsi = RichSequence.IOTools.readINSDseqDNA(br, ns);

        // Since a single file can contain more than a sequence, you need to iterate over
        // rsi to get the information.
                    while (rsi.hasNext()) {
                        RichSequence seq = rsi.nextRichSequence();
                        RichSequence.IOTools.writeFasta(new 
                                     FileOutputStream(new File(filePath+fastaExt)), seq, ns);
                        System.out.println(
                                seq.toString() +
                                " has " + seq.countFeatures() + 
                                " features");
                    }

    }
    catch(Exception be){
        be.printStackTrace();
        System.exit(-1);
    }
}

}

for more you should refer to the BioJava CookBook Here