The Kabat Numbering Scheme
The Kabat numbering scheme is a widely used standard for numbering residues in antibodies, ensuring consistency across different studies. However, the scheme has several limitations. Firstly, the numbering was based on early sequence data, which was relatively limited, leading to misalignments in the position of insertions within CDR-L1 and CDR-H1. As a result, topologically similar residues in these loops are not assigned the same number.
Secondly, the rigid nature of the numbering system creates challenges. For instance, in the long CDR-H3 region, insertions are numbered between residues H100 and H101, with letters extending up to K (e.g., H100, H100A...H100K, H101). When there are more residues than this, there is no standardized way to number them. This issue arises in other regions as well.
The Chothia Numbering Scheme
The Chothia numbering scheme addresses some of the limitations of the Kabat scheme by placing insertions in CDR-L1 and CDR-H1 at structurally conserved positions. This results in topologically equivalent residues receiving the same label, unlike in the Kabat system.
However, there are some disadvantages. Firstly, the Kabat scheme has become so widely adopted that the shift to Chothia’s method can cause confusion. Additionally, in their 1989 Nature paper, Chothia and colleagues moved the insertion site in CDR-L1 from L30 to L31. Upon examining loop conformations, it is clear that L30 is the correct position.
It is important to note that in their later work (Al-Lazikani et al., 1997, JMB 273, 927-948), Chothia's group returned to using L30 as the insertion site for CDR-L1.
The Martin (Enhanced Chothia) Numbering Scheme
The Martin numbering scheme enhances the Chothia system by refining the locations of insertions (indels) in both CDR-L1 and CDR-H1. The main difference lies in the positioning of indels within the framework regions.
A notable change is the movement of the indel site at H82a,b,c, which is commonly seen in many antibodies, to the more structurally accurate position at H72a,b,c. Furthermore, the Martin scheme introduces an indel site at L52 in CDR-L2, which corresponds to the AHo numbering scheme and reflects an area of rare length variation in the structure.
How to Identify the CDRs from Sequences
To identify the CDRs (both Kabat and Chothia) in an antibody sequence, certain rules can be followed. These rules are generally reliable, but it’s important to note that there are rare exceptions. For instance, the human heavy chain EU sequence lacks the typical Trp-Gly after CDR-H3. Cysteine residues, however, are consistently the most conserved marker.
CDR-L1
Start: Around residue 24
Residue before: Always a Cys
Residue after: Always a Trp. Typically Trp-Tyr-Gln, but also, Trp-Leu-Gln, Trp-Phe-Gln, Trp-Tyr-Leu
Length: 10 to 17 residues
CDR-L2
Start: Always 16 residues after the end of L1
Residues before: Typically Ile-Tyr, but also, Val-Tyr, Ile-Lys, Ile-Phe
Length: Always 7 residues (except NEW (7FAB) which has a deletion in this region)
CDR-L3
Start: Always 33 residues after the end of L2 (except NEW (7FAB) which has the deletion at the end of CDR-L2)
Residue before: Always Cys
Residues after: Always Phe-Gly-XXX-Gly
Length: 7 to 11 residues
CDR-H2
Start: Always 15 residues after the end of CDR-H1 (Kabat/AbM definition)
Residues before: Typically Leu-Glu-Trp-Ile-Gly, with several variations
Residues after: Lys/Arg-Leu/Ile/Val/Phe/Thr/Ala-Thr/Ser/Ile/Ala
Length: Kabat definition: 16 to 19 residues; AbM (and recent Chothia) definition: 7 residues earlier
CDR-H3
Start: Always 33 residues (sometimes 30 residues) after CDR-H2, and always 3 residues after Cys
Residue before: Always Cys-XXX-XXX (typically Cys-Ala-Arg)
Residues after: Always Trp-Gly-XXX-Gly
Length: 3 to 25 residues (longer in bovine antibodies)
At AbinScience
AbinScience, established in 2023 and based in the Innovation Technology Center in Strasbourg, France, specializes in the development and production of life science research reagents. Committed to “Empowering Bioscience Discovery,” AbinScience offers high-quality, innovative biological reagents and technical solutions to researchers worldwide. We provide advanced tools for antibody research, including precise antibody numbering, structural modeling, and CDR prediction. Our solutions are designed to simplify complex antibody analyses, helping researchers effectively navigate various numbering systems such as Kabat, Chothia, and Martin. By integrating our tools into your research workflow, you can improve accuracy, save time, and increase overall efficiency in your antibody studie
