Atom Nomenclature for AKN

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 AKN

Atom Name (V3) Atom Name (V2)
C1 C1
C3 C2
C4 C3
C5 C4
C7 C5
C9 C6
O6 O1
O2 O2
O8 O3
N10 N1
C11 C7
N12 N2
C13 C8
C14 C9
N15 N3
C16 C10
C17 C11
O18 O4
C19 C12
O20 O5
C21 C13
C22 C14
O23 O6
C24 C15
N25 N4
C26 C16
O27 O7
C28 C17
O29 O8
C30 C18
O31 O9
O32 O10
O33 O11
N37 N5
C35 C19
O36 O12
C37 C20
C38 C21
C39 C22
O40 O13
H1 H1
H2 H2
H3 H3
H4 H4
H5 H5
H6 H6
H7 H7
H8 H8
H9 H9
H10 H10
H12 H12
H13 H13
H14 H14
H15 H15
H16 H16
H17 H17
H18 H18
H20 H20
H21 H21
H22 H22
H23 H23
H24 H24
H25 H25
H26 H26
H27 H27
H28 H28
H29 H29
H31 H31
H32 H32
H33 H33
H34 H34
H35 H35
H36 H36
H37 H37
H38 H38
H39 H39
H40 H40
H42 H42
H43 H43
H44 H44
H45 H45
H46 H46
H47 H47