Atom Nomenclature for ID5

The atom nomenclature in PDB data files was revised with the release of data in the PDB Format Version 3.0. These changes make the PDB atom names used by PDB compliant with existing IUPAC nomenclature for standard amino acid and nucleotides (Pure & Appl. Chem., 70, 117-142, 1998) with the exception of the well established convention for C-terminal atoms OXT and HXT. A small number of additional changes were introduced in Version 3 to make atom labeling more conventional. The following chemical diagrams and tables provide the correspondences between atom names used in Version 3 and Version 2 PDB formats.

Labeled Chemical Diagrams

Chemical diagram with format V3 atom labels (heavy atoms)
Chemical diagram with format V3 atom labels (all atoms)
Chemical diagram with format V2 atom labels (heavy atoms)
Chemical diagram with format V2 atom labels (all atoms)

Atom Name Correspondences for ID5

Atom Name (V3) Atom Name (V2)
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
C7 C7
F8 F8
F9 F9
C11 C11
C13 C13
F14 F14
O15 O15
O16 O16
C18 C18
C20 C20
N21 N21
S22 S22
F23 F23
C24 C24
C25 C25
C26 C26
C27 C27
C28 C28
C29 C29
C32 C32
O33 O33
O34 O34
N36 N36
H2 H2
H3 H3
H6 H6
H181 1H18
H182 2H18
H201 1H20
H202 2H20
H28 H28
H33 H33
H36 H36