Atom Nomenclature for KT3

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 KT3

Atom Name (V3) Atom Name (V2)
N2A 2N
CD1 1CD
OEB 1OE1
CG1 1CG
CB1 1CB
CA1 1CA
C1A 1C
O11 1OXT
O1A 1O
N1A 1N
C C
O O
C14 C14
C15 C15
C16 C16
C13 C13
C12 C12
C11 C11
C10 C10
C5 C5
C6 C6
F2 F2
F1 F1
F3 F3
OA2 OA2
OA1 OA1
C1 C1
C2 C2
C3 C3
C4 C4
C7 C7
N8 N8
C9 C9
O1 O1
N3 N3
C8 C8
N2 N2
N1 N1
OEN 3OE2
OED 3OE1
CD3 3CD
CG3 3CG
CB3 3CB
CA3 3CA
C3A 3C
O3 3O
O12 3OXT
N3A 3N
OEC 2OE1
CD2 2CD
CG2 2CG
CB2 2CB
CA2 2CA
C2A 2C
O2 2O
O13 2OXT
H2 2H
HG11 1HG1
HG21 1HG2
HB11 1HB1
HB21 1HB2
HA1A 1HA
HXT1 1HXT
H1 1H
H15 H15
H16 H16
H13 H13
H12 H12
H10 H10
HA2 HA2
HA1 HA1
H11 1H1
H12A 2H1
H21 1H2
H22 2H2
H31 1H3
H32 2H3
HN81 1HN8
HN82 2HN8
HO1 HO1
HN21 1HN2
HN22 2HN2
HE23 3HE2
HG13 3HG1
HG23 3HG2
HB13 3HB1
HB23 3HB2
HA3 3HA
HXT3 3HXT
H3 3H
HG12 2HG1
HG22 2HG2
HB12 2HB1
HB22 2HB2
HA2A 2HA
HXT2 2HXT