Go to the PDB WWW page . That should download a file called 1CDW.pdb to your hard drive. These lines give the atom number, atom name, residue name, residue number, x coordinate, y coordinate, z coordinate, occupancy, and thermal factor of every atom in the protein. The thermal factor tells you about relative mobility. CA is an alpha carbon.
Every amino acid has an alpha carbon.
Those atoms are part of the polypeptide backbone. That atom is part of the R-group of valine. Hydrogen atoms are missing, because hydrogen atoms are not observed by x-ray diffraction of large molecules like proteins. Some PDB files contain hydrogen atoms, but they were put there via modeling and geometric considerations, not from the diffraction data. What is the secondary structure of these three residues.