Most of the definitions in the table below are courtesy of the PDB Glossary of Technical Terms.

Term Definition
Active site, binding site, or site The region of a protein that binds substrates and that is involved in chemical reactions. Generally an active site contains very specific amino acids that participate in the binding.
Alpha carbon The carbon in an amino acid to which the side chain is attached.
Alpha helix or helix A secondary structural motif of a protein. It is characterized by hydrogen bonds between the carbonyl group (-C=O) of one amino acid and the amino (N-H) group of the amino acid 4 residues below it along the helix. The helix makes one complete turn every 3.6 amino acids.
Atom and bond Base units for displaying molecular structure.
B-factor or temperature factor A measure of how much the position of an atom deviates from that given in the atomic coordinates. This deviation is due to thermal motion and crystal imperfections. Temperature factors are also termed B-factors.
Beta sheet A secondary structural motif of a protein. It is characterized by 2 or more amino acid chains lying side-by-side where hydrogen bonds are formed between carbonyl groups (C=O) of one chain and amino groups (N-H) of the adjacent chain. This arrangement forms a sheet-like structure.
CATH A hierarchical classification of protein structural relationships which groups proteins at four major levels: Class©, Architecture(A), Topology(T) and Homologous superfamily (H).
Chain A single biopolymer, either a polypeptide (protein) or polynucleotide (DNA, RNA).
CPK model A space filling three-dimensional representation of a molecule. Given the centers of the molecule atoms and the relative van der Waals radii, a spherical CPK-type representation of a molecule can be built.
Data (NMR) In NMR spectroscopy, the initial data collected include high-resolution multidimensional NMR spectra which reveal correlations between atoms that lie either within a few bonds of each other (J coupling) or within a short distance of each other (NOE coupling). NMR resonances are then assigned to specific atoms in the molecule and couplings are assigned to pairs or groups of atoms. These couplings are then used to produce a list of restraints that specify that particular atoms in the final model be near each other. Finally, a computer program is used to produce a model of the molecule which fits all of the restraints.
Data (X-ray) In X-ray crystallography, the initial data include the measured positions and intensities of the reflections in the diffraction pattern produced by the macromolecular crystal. The relative phases of the waves that produced the diffraction pattern are also determined. An electron-density map of the molecule is then computed from the positions, intensities and phases of all of the reflections. A model of the molecule contained within the crystal is then built to fit the electron-density map.
Disordered regions (NMR) In NMR spectroscopy, disordered regions of molecules result in high variability between the models of the ensemble. Atom positions in these regions are very uncertain.
Disordered regions (X-ray) In X-ray crystallography, disordered regions of molecules appears as weak regions of electron density and as regions with high temperature factors. Atom positions in these regions are very uncertain.
Disulfide bond Covalent bond formed between the sulfur atoms of two cysteine residues in a protein. Disulfide bonds often stabilize protein structure or link multiple proteins in a complex.
Gene Ontology (GO) A bioinformatics initiative to standardize the representation of gene and gene product attributes across species and databases. The ontology covers three domains: cellular component, molecular function and biological process.
Insertion code A non-numerical component of the residue identifier that historically exists to shift the natural numbering of residues so that key residues maintain the same index number across homologous proteins.
Kabsch and Sander DSSP method (KSDSSP, KSD) Features created by Protean 3D and shown/hidden on the Sequence View via the Features Panel.

KSDSSP is an implementation of the method for assigning secondary structure developed by Kabsch and Sander (1983). In brief, the algorithm identifies hydrogen bonds along the backbone of a protein structure, then classifies the secondary structure based on the observed hydrogen bonding patterns.

The original DSSP algorithm recognizes eight types of secondary structure (G = 3:10 helix, H = alpha helix, I = pi helix, E = beta strand, B = beta bridge, T = turn, S = high curvature, L = loop/other). KSDSSP reports three types of secondary structures: helix/H (G, H, I), strand/S (E, B), coil/C (T, S, L). Protean 3D uses the HSC classification from KSDSSP and creates features of helices and strands.

Reference: Kabsch W. and Sander C. (1983) "Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features" Biopolymers 22:2577.
Ligand A molecule that binds specifically to another molecule (usually a protein or nucleic acid) to form a complex. A ligand can be another protein, but is often a small molecule.
Model A conformation of a set of molecules, including positions of atoms.
Nuclear Magnetic Resonance (NMR) Nuclear magnetic resonance is a property that magnetic active nuclei have in a magnetic field when responding to applied electromagnetic pulses or perturbations. The measurements of such responses provide rich structural, dynamic, and kinetic information about the molecule.
Occupancy (X-ray) The occupancy of an atom is a measure of the fraction of molecules in the crystal in which the atom is actually present in the position specified by the model. If all of the molecules in the crystal are identical, then occupancies for all of the atoms are 1.00. Otherwise, two or more conformations may be observed for a small region of an atom, such as a side chain. The atoms are then given occupancies equal to the fraction of side chains in each distinct conformation.
Protein Data Bank (PDB) The single repository of experimentally determined structures of proteins, nucleic acids and complex biomolecular assemblies as managed by the Worldwide Protein Data Bank. PDB can also refer to a particular file format for describing structures.
Residue An amino or nucleic acid that is part of a biopolymer by means of a condensation reaction.
Secondary structure The arrangement a protein arising from hydrogen bonding interactions within contiguous segments of the polypeptide backbone. The two main types of secondary structure are the alpha helix and the beta-pleated sheet.
Side chain The variable group in an amino acid that is attached to the alpha carbon.
Structure A non-empty set of models of a set of molecules.
Temperature factor A measure of how much the position of an atom deviates from that given in the atomic coordinates. This deviation is due to thermal motion and crystal imperfections. Temperature factors are also termed B-factors.
Theoretical model Theoretical models are produced by methods other than X-ray diffraction and NMR spectroscopy. Theoretical models include homology models and models derived from simulations of folding and molecular dynamics.
X-ray crystallography A method used to determine the detailed three-dimensional structure of molecules present in a crystal in which an X-ray beam is aimed at the crystal and the resulting scattered rays are studied.

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