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Input a PDB code and/or chain ID to find the antibody CDRs.
The PDB code is not case sensitive while the chain is case sensensitive.
That is, 1P7K is same as 1p7k, but 1P7KL is not same as 1P7Kl. Figure 1 shows the PDB input page.
Figure 1: PDB input page
Figure 2 shows the search resultfor 1P7K and chain L. There are 3 CDRs: L1, L2, L3,
and 3 clusters: L1-11-1, L2-8-1 and L3-9-cis7-1. Cluster is formated as CDR-length-cluster number.
Figure 2: CDRs and clusters for 1P7K and chain L.
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Figuer 3 shows all clusters in 6 CDRs.
Cluster with * are new CDR lengths or cis/trans conformations of existing lengths that have not yet been clustered.
Reclustering of existing lengths and clustering of new lengths will occur by the Antibody Team every few months
once enough new data is available from the PDB.
Select a cluster to retrieve the structures with CDRs in the cluster.
Figure 3: Cluster select page.
Figure 4 shows a summary table for the input cluster L1-11-1 and all structures in the cluster.
Click "Show Non-Redundant Chains Only" to display only the structures with unique sequences and best resolutions.
Click the same button to display all structures again.
"Export csv File" is to export the data in the table into a csv file which can be saved into the local machine.
Figure 4: The structures in cluster L1-11-1
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Select a CDR to retrieve all structures containing the CDR. Figure 5 shows all CDRs and their lengths.
Figure 5: CDR select page.
Figure 6 shows the structures and CDR clusters for CDR L1. "Show Non-Redundant Chains Only" is to show
the structures with unique sequences and best resolutions. Click the same button to display all structures again.
"Export csv File" is to export the data in the table into a csv file which can be saved into the local machine.
Figure 6: Structures and clusters with CDR L1.
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Select a species and germline to retrieve framework/CDRs information of the PDB structures with the species and germline.
There are 3 ways to choose a germline:
1. Framework
The species and germline of the framework of PDB structures are the selected species and germline,
while the species and germlines of CDRs may not same as the frameworks'.
2. CDRs
The species and germline of the CDRs of PDB structures are the selected species and germline,
while the species and germlines of frameworks may not be same as the CDRs'.
3. Both
The species and germline of both framework and CDRs are the selected species and germline. So they are always same.
Figure 7 shows the all germlines in the current databases. For each item, the first word is species, the second one is germline IG class.
Figure 7: Germline select page.
Figure 8 shows the species, germlines and clusters of both framework and CDRs for Human species and germline IG class IGHV1.
The framework and CDRs are from the same species and germlines. CDR species and germline is for both CDR1 and CDR2.
Figure 8: The result table of germline search: Human + IGHV1 for both framework and CDRs.