Atom Nomenclature for CKK

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 CKK

Atom Name (V3) Atom Name (V2)
N14 N14
C17 C17
C16 C16
C15 C15
C19 C19
C20 C20
C21 C21
C23 C23
C12 C12
C27 C27
C33 C33
F1 F1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
C7 C7
C8 C8
C9 C9
O10 O10
N11 N11
O13 O13
F18 F18
O22 O22
N24 N24
C25 C25
N26 N26
N28 N28
C29 C29
C30 C30
C31 C31
C32 C32
N34 N34
C35 C35
C36 C36
C37 C37
C38 C38
N39 N39
HN14 HN14
H16 H16
H19 H19
H20 H20
H33 H33
H33A H33A
H3 H3
H4 H4
H5 H5
H6 H6
H8 H8
H8A H8A
HN11 HN11
H25 H25
H29 H29
H30 H30
H32 H32
H32A H32A
H35 H35
H35A H35A
H36 H36
H36A H36A
H37 H37
H38 H38
H38A H38A
HN39 HN39
HN3A HN3A