Atom Nomenclature for GTT

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 GTT

Atom Name (V3) Atom Name (V2)
N1 N1
CA1 CA1
C1 C1
O11 O11
O12 O12
CB1 CB1
CG1 CG1
CD1 CD1
OE1 OE1
N2 N2
CA2 CA2
C2 C2
O2 O2
CB2 CB2
SG2 SG2
N3 N3
CA3 CA3
C3 C3
O31 O31
O32 O32
HN11 HN11
HN12 HN12
HN13 HN13
HA1 HA1
HO2 HO2
HB11 HB11
HB12 HB12
HG11 HG11
HG12 HG12
HN2 HN2
HA2 HA2
HB21 HB21
HB22 HB22
HSG HSG
HN3 HN3
HA31 HA31
HA32 HA32
HO3 HO3