Atom Nomenclature for 6OB

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 6OB

Atom Name (V3) Atom Name (V2)
C10 C10
C18 C18
C17 C17
C16 C16
C15 C15
C14 C14
C13 C13
C12 C12
C11 C11
C9 C9
C8 C8
C7 C7
C6 C6
O3 O3
C5 C5
C4 C4
C3 C3
C2 C2
C1 C1
O1 O1
O2 O2
OXT OXT
H10 H10
H111 1H11
H112 2H11
H9 H9
H181 1H18
H182 2H18
H183 3H18
H171 1H17
H172 2H17
H161 1H16
H162 2H16
H151 1H15
H152 2H15
H141 1H14
H142 2H14
H13 H13
H12 H12
HA HA
HA1 1HA
HB2 2HB
HB1 1HB
HC2 2HC
HC1 1HC
HD2 2HD
HD1 1HD
HE2 2HE
HE1 1HE
HF2 2HF
HB HB
HOT HOT