Atom Nomenclature for 1M5

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 1M5

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
O7 O7
C8 C8
C9 C9
C10 C10
C11 C11
C12 C12
C13 C13
C14 C14
N15 N15
C16 C16
N17 N17
N18 N18
O19 O19
C20 C20
C21 C21
C22 C22
C23 C23
C24 C24
C25 C25
CL1 CL1
H1 H1
H2 H2
H3 H3
H4 H4
H5 H5
H6 H6
H7 H7
H8 H8
H9 H9
H10 H10
H11 H11
H12 H12
H13 H13
H14 H14
H15 H15
H16 H16
H17 H17
H18 H18
H19 H19
H20 H20