Atom Nomenclature for LK4

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 LK4

Atom Name (V3) Atom Name (V2)
N31 N31
C30 C30
C27 C27
C28 C28
C29 C29
C26 C26
C25 C25
C24 C24
C23 C23
O22 O22
C20 C20
C19 C19
C18 C18
C21 C21
C15 C15
C16 C16
C17 C17
C14 C14
C13 C13
C12 C12
S11 S11
O33 O33
O32 O32
N N
CA CA
C C
O O
OXT OXT
CB CB
CG CG
CD CD
OE1 OE1
OE2 OE2
H28 H28
H26 H26
H29 H29
H25 H25
H231 1H23
H232 2H23
H19 H19
H21 H21
H18 H18
H14 H14
H17 H17
H13 H13
H H
HA HA
HBC1 1HBC
HBC2 2HBC
HXT HXT
HGC1 1HGC
HGC2 2HGC
HE2 HE2