Table 5. Summary table for the clustering of CDR-L3.
| Cluster | Population | Unique sequences |
Medoid PDB entry |
Medoid Ramachandran conformation |
Level-3 clusters |
Level-2 clusters |
Cluster diameter (Å) (furthest members) |
Best resolution in cluster (Å) (PDB) |
Species in cluster | Isotype |
|---|---|---|---|---|---|---|---|---|---|---|
| CDR-L3 5-residues, total population: 10, total unique sequences: 4, clusters: 1, outliers/singletons: 0, Av.Silhouette: N/A | ||||||||||
| L3-5-I | 10 | 4 (100%) | 3NGB_C | BBGAB | 2 | 1 | 0.26 (3U7W_L-3Sé_L) | 1.9 (3SE8_L) | HUMAN | κ |
| CDR-L3 7-residues, total population: 5, total unique sequences: 2, clusters: 1, outliers/singletons: 0, Av.Silhouette: N/A | ||||||||||
| L3-7-I | 5 | 2 (100%) | 3IU3_L | BBDDDLP | 4 | 1 | 0.49 (1mim_L-1dfb_L) | 2.6 (1mim_L) | HUMAN, MOUSE | κ |
| CDR-L3 8-residues, total population: 138, total unique sequences: 43, clusters: 6, outliers/singletons: 2, Av.Silhouette: 0, 56 | ||||||||||
| L3-8-I | 105 | 28 (65%) | 1q9w_C | BPDABGBB | 13 | 4 | 0.76 (3KJ4_L-1m71_A) | 1.45 (1q9r_A) | HUMAN, MOUSE, RAT |
κ |
| L3-8-II | 12 | 6 (14%) | 1tzh_L | BPDBBPBP | 9 | 5 | 1.18 (3DGG_C-1e6j_L) | 1.77 (2fat_L) | HUMAN, MOUSE | κ |
| L3-8-III | 7 | 4 (9%) | 3hfl_L | BPDPABPB | 7 | 4 | 0.98 (1ORS_A-1ehl_L) | 1.7 (1YQV_L) | MOUSE | κ |
| L3-8-IV | 5 | 2 (5%) | 3JWD_L | BPDADPDP | 3 | 3 | 0.66 (2J88_L-1rz7_L) | 2.0 (1rz7_L) | HUMAN, MOUSE | κ |
| L3-8-V | 4 | 3 (7%) | 1za3_A | BPAABPDP | 4 | 4 | 0.85 (3DGG_A-1za3_L) | 2.3 (3DGG_A) | HUMAN | κ |
| L3-8-VI | 3 | 1 (2%) | 3MCL_L | BBAAPBPA | 1 | 1 | 0.24 (3O11_A-3O11_L) | 1.7 (3MCL_L) | CHIMERA OF MOUSE/HUMAN |
κ |
| CDR-L3 9-residues, total population: 1725, total unique sequences: 358, clusters: 6, outliers/singletons: 5, Av.Silhouette: 0, 65 | ||||||||||
| L3-9-I | 1528 | 328 (92%) | 1dqj_A | BBDABPPPB | 153 | 34 | 1.72 (1maj_A_11-1kel_L) | 1.2 (3D9A_L) | HUMAN, MOUSE, RAT, RABBIT, CHIMPANZEE, SYNTHETIC HUMANIZED ANTIBODY, CHIMERA OF MOUSE/HUMAN |
κ |
| L3-9-II | 136 | 20 (6%) | 2XZQ_L | BBBBGDBPB | 36 | 8 | 1.36 (2E27_L-1pw3_B) | 1.5 (1oaq_L) | HUMAN, MOUSE, RAT, SYNTHETIC HUMANIZED ANTIBODY, CHIMERA OF MOUSE/HUMAN |
κ, λ |
| L3-9-III | 40 | 8 (2%) | 1op3_L | BPBBADBBB | 15 | 8 | 1.4 (8fab_C-3C08_L) | 1.75 (1op3_L) | HUMAN, MOUSE, CHIMERA OF MOUSE/HUMAN |
κ, λ |
| L3-9-IV | 8 | 1 (0,3%) | 3MLR_L | BBBBBBBPA | 3 | 2 | 1.24 (3MLV_M-3MLS_M) | 1.8 (3MLR_L) | HUMAN | λ |
| L3-9-V | 6 | 1 (0,3%) | 3RU8_L | BBBGLLBBB | 2 | 2 | 0.34 (1n0x_L-1hzh_M) | 1.8 (1n0x_L) | HUMAN | κ |
| L3-9-VI | 2 | 1 (0,3%) | 3FN0_L | BBGBPBABA | 1 | 1 | 0.23 (3Q1S_L-3FN0_L) | 1.8 (3FN0_L) | HUMAN | κ |
| CDR-L3 10-residues, total population: 113, total unique sequences: 27, clusters: 12, outliers/singletons: 6, Av.Silhouette: 0, 59 | ||||||||||
| L3-10-I | 22 | 2 (7%) | 3MUG_I | BBPBADLPBB | 4 | 2 | 0.76 (3MUH_L-3LRS_B) | 1.8 (3U2S_L) | HUMAN | λ |
| L3-10-II | 20 | 2 (7%) | 1MCD_A | BBPBGLLBBP | 15 | 9 | 1.28 (1mcc_A-1lil_B) | 2.0 (2mcg_2) | HUMAN, SEAL | λ |
| L3-10-III | 9 | 4 (15%) | 3B5G_A | BBBPAALPPB | 4 | 1 | 1.19 (3GO1_L-2XZA_L) | 1.36 (2XZC_L) | HUMAN | λ |
| L3-10-IV | 9 | 4 (15%) | 3EYO_C | BBDABBPPPB | 5 | 2 | 0.51 (3F12_A-3eyq_C) | 1.8 (1jgu_L) | MOUSE | κ |
| L3-10-V | 7 | 3 (11%) | 2dd8_L | BBBBADDGPB | 5 | 1 | 1.06 (3UJI_L-3G6A_L) | 1.6 (3UJI_L) | HUMAN | λ |
| L3-10-VI | 5 | 1 (4%) | 3MLY_L | BBPBAALBPB | 1 | 1 | 0.24 (3MLZ_L-3MLY_M) | 1.7 (3MLY_L) | HUMAN | λ |
| L3-10-VII | 5 | 3 (11%) | 3TV3_L | BBPBGADPBB | 4 | 3 | 0.84 (3TWC_L-1mcw_M) | 1.29 (3TV3_L) | HUMAN | λ |
| L3-10-VIII | 4 | 1 (4%) | 2fl5_A | BBBPADLPPB | 2 | 2 | 0.18 (2fl5_C-2fl5_L) | 3.0 (2fl5_L) | HUMAN | λ |
| L3-10-IX | 4 | 1 (4%) | 1mqk_L | BPDBGBPPBB | 3 | 1 | 0.31 (3HB3_D-1qle_L) | 1.28 (1mqk_L) | MOUSE | κ |
| L3-10-X | 3 | 1 (4%) | 3IDY_L | BBDABBPPBB | 2 | 1 | 0.23 (3IDY_C-3IDX_L) | 2.5 (3IDX_L) | HUMAN | κ |
| L3-10-XI | 2 | 1 (4%) | 1i7z_A | BPBBABPPBB | 2 | 1 | 0.12 (1i7z_A-1i7z_C) | 2.3 (1i7z_A) | CHIMERA OF MOUSE/HUMAN |
κ |
| L3-10-XII | 17 | 3 (11%) | 1mcn_B | BBPPPADBBP | 17 | 15 | 1.55 (1mch_B-1lil_A) | 2.0 (2mcg_1) | HUMAN, SEAL | λ |
| CDR-L3 11-residues, total population: 142, total unique sequences: 38, clusters: 9, outliers/singletons: 7, Av.Silhouette: 0, 64 | ||||||||||
| L3-11-I | 74 | 24 (63%) | 3G04_A | BBPBAADLBPB | 27 | 2 | 1.72 (3MAC_L-2rhe_A) | 1.43 (3N9G_L) | HUMAN, MOUSE, HAMSTER |
κ, λ |
| L3-11-II | 24 | 1 (3%) | 1yym_Q | BPDAPBPPBPB | 6 | 3 | 0.34 (1yym_L-1g9n_L) | 1.99 (2NY1_C) | HUMAN | κ |
| L3-11-III | 11 | 3 (8%) | 2OMN_A | BBPBAPABABB | 7 | 3 | 1.01 (3GHE_L-2OMB_D) | 1.5 (3KDM_L) | HUMAN | λ |
| L3-11-IV | 8 | 1 (3%) | 2QR0_G | BBBLPDDBABB | 8 | 4 | 0.36 (2QR0_S-2QR0_K) | 3.5 (2QR0_A) | HUMAN | κ |
| L3-11-V | 5 | 2 (5%) | 3NH7_M | BBPBAPLLBBB | 4 | 3 | 0.59 (4bjl_A-3NH7_O) | 2.4 (4bjl_A) | HUMAN | λ |
| L3-11-VI | 4 | 2 (5%) | 2JB6_A | BBBPAALDBBB | 2 | 1 | 0.77 (3UJJ_L-2JB5_L) | 2.0 (3UJJ_L) | HUMAN | λ |
| L3-11-VII | 4 | 1 (3%) | 3EFF_C | BBDAPBBLAGB | 4 | 4 | 0.6 (3PJS_C-3EFF_A) | 3.8 (3EFF_A) | MOUSE | κ |
| L3-11-VIII | 3 | 1 (3%) | 2b1h_L | BBPBDAALBPB | 2 | 1 | 0.2 (2b1a_L-2b0s_L) | 2.0 (2b1h_L) | HUMAN | λ |
| L3-11-IX | 2 | 1 (3%) | 1nfd_E | BBBBGAALPPB | 1 | 1 | 0.17 (1nfd_E-1nfd_G) | 2.8 (1nfd_E) | MOUSE | λ |
| CDR-L3 12-residues, total population: 19, total unique sequences: 6, clusters: 4, outliers/singletons: 0, Av.Silhouette: 0, 73 | ||||||||||
| L3-12-I | 6 | 1 (17%) | 2X7L_D | BBGBAAGADGBB | 1 | 1 | 0.04 (2X7L_K-2X7L_B) | 3.17 (2X7L_B) | Not available | κ |
| L3-12-II | 6 | 1 (17%) | 1q1j_L | BBBPAPAALPPB | 2 | 1 | 0.31 (3GHB_L-3C2A_M) | 2.1 (3C2A_L) | HUMAN | λ |
| L3-12-III | 4 | 2 (33%) | 3LZF_L | BBPBAPGAGBPB | 3 | 3 | 0.9 (3QHZ_M-3GBN_L) | 1.55 (3QHZ_M) | HUMAN | λ |
| L3-12-IV | 3 | 2 (33%) | 3LQA_L | BBPBAPGAAGPB | 3 | 3 | 1.35 (3P30_L-3LMJ_L) | 2.2 (3LMJ_L) | HUMAN | λ |
| CDR-L3 13-residues, total population: 12, total unique sequences: 2, clusters: 3, outliers/singletons: 1, Av.Silhouette: 0, 71 | ||||||||||
| L3-13-I | 6 | 1 (50%) | 2OTU_A | BBBBPPAABPBBB | 1 | 1 | 0.18 (2OTW_C-2OTU_G) | 1.68 (2OTU_A) | MOUSE | λ |
| L3-13-II | 3 | 1 (50%) | 2QHR_L | BBBBBBLLBPBBB | 3 | 3 | 0.97 (3FFD_B-2GSG_A) | 2.0 (2QHR_L) | MOUSE | λ |
| L3-13-III | 2 | 1 (50%) | 3MLW_L | BBBPDABABPPPB | 2 | 2 | 0.48 (3MLW_L-3MLW_M) | 2.7 (3MLW_L) | HUMAN | λ |
|
Total
(level-1 clusters only) |
2143 | 393 | 153 | |||||||