Atom Nomenclature for TPP

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 TPP

Atom Name (V3) Atom Name (V2)
N1' N1'
C2' C2'
CM2 CM2
N3' N3'
C4' C4'
N4' N4'
C5' C5'
C6' C6'
C7' C7'
N3 N3
C2 C2
S1 S1
C5 C5
C4 C4
CM4 CM4
C6 C6
C7 C7
O7 O7
PA PA
O1A O1A
O2A O2A
O3A O3A
PB PB
O1B O1B
O2B O2B
O3B O3B
HM21 HM21
HM22 HM22
HM23 HM23
HN41 HN41
HN42 HN42
H6' H6'
H7'1 H7'1
H7'2 H7'2
H2 H2
HM41 HM41
HM42 HM42
HM43 HM43
H61 H61
H62 H62
H71 H71
H72 H72
HOA2 HOA2
HOB2 HOB2
HOB3 HOB3