Sequence Similarity Clusters for the Entities in PDB 3JWD

Entity #1 | Chains: A,B
HIV-1 GP120 ENVELOPE GLYCOPROTEIN protein, length: 379 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 1 1 34823
95 % 1 2 22307 Flexibility: Low
Max RMSD: 0.6, Avg RMSD: 0.6
PDBFlex
90 % 1 2 21654
70 % 69 129 183
50 % 69 129 223
40 % 69 129 242
30 % 69 132 249
Entity #2 | Chains: C,D
T-cell surface glycoprotein CD4 protein, length: 184 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 17 38 725
95 % 20 43 872 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 1.2
PDBFlex
90 % 20 43 904
70 % 20 43 932
50 % 20 43 968
40 % 20 43 995
30 % 20 43 975
Entity #3 | Chains: L,O
FAB 48D LIGHT CHAIN protein, length: 213 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 2 4 15714
95 % 83 192 62 Flexibility: Low
Max RMSD: 6.5, Avg RMSD: 2.2
PDBFlex
90 % 420 762 2
70 % 1325 2416 1
50 % 2707 4892 1
40 % 2707 4892 1
30 % 3100 5759 1
Entity #4 | Chains: H,P
FAB 48D HEAVY CHAIN protein, length: 220 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 2 4 15650
95 % 2 5 9448 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 1.0
PDBFlex
90 % 2 5 9349
70 % 1313 2366 2
50 % 2708 4892 1
40 % 2708 4892 1
30 % 3101 5759 1

Instructions

In the table for each entity, view a list of similar sequences by selecting the link associated with the percentage cutoff.



View more detailed documentation on the redundancy reduction and sequence clustering procedure used by RCSB PDB.

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Rank PDB ID Entity ID Chains Description Details Taxonomy EC Number
1 5UCB 2 L Fab Light Chain 9606
2 3HC4 2 L IMMUNOGLOBULIN IGG1 FAB, LIGHT CHAIN 9606
3 5UEA 3 B, L Fab Light Chain 9606
4 5TDN 1 A, C anti-HER2 Fab Light Chain 9606
5 3NCJ 1 L Fab15 Mut8 light chain 9606
6 3HC3 2 L IMMUNOGLOBULIN IGG1 FAB, HEAVY CHAIN 9606
7 3NA9 1 L Fab15 light chain 9606
8 5UEK 3 L Fab 12E Light Chain 9606
9 3NAA 1 L Fab15 Mut5 light chain 9606
10 6BHZ 2 L, M Trastuzumab Anti-HER2 Fab Light Chain D185A 9606
11 5IT2 2 L light chain 9606
12 6B14 2 L Light chain of Fab BL3-6S97N 10090
13 5XHG 1 A, C polypeptide(L) 562
14 6BI2 2 L, M Trastuzumab Anti-HER2 Fab Light Chain 9606
15 5TDO 1 A, C anti-HER2 Fab Light Chain 9606
16 3P0Y 3 L Fab DL11 light chain 9606
17 6ELE 2 B, L fAB light chain 9606
18 3NAC 1 L Fab15 Mut7 light chain 9606
19 5WUV 1 L light chain 9606
20 5TDP 1 A, C anti-HER2 Fab Light Chain 9606
21 1L7I 1 L chimera of Fab2C4: "humanized" murine monoclonal antibody The chimera consists of the human Ig and the original murine sequence light chain (residues 1-214) 9606
22 5XKU 2 B HNIgGA6 light chain 9606
23 3SOB 1 L antibody light chain 9606
24 4KQ3 1 L CNTO3186 light chain Fab 9606
25 3HC0 2 B, L IMMUNOGLOBULIN IGG1 FAB, HEAVY CHAIN 9606
26 6ELJ 2 B, L fAB light chain 9606
27 5JW5 2 B, L MEDI8852 Light chain 9606
28 5VAG 2 B Light chain of antibody m826 9606
29 6ELL 2 B, L fAB light chain 9606
30 2HFF 1 A, L CB2 Fab, light chain 9606
31 1VGE 1 L TR1.9 FAB FAB FRAGMENT OF A HUMAN IGG1 KAPPA AUTOANTIBODY 9606
32 5GGV 1 L light chain 9606
33 5BJZ 3 H, L Synthetic antibody, Fab fragment, Light Chain 9606
34 2R8S 2 L Fab light chain 10090
35 4HKZ 1 A Trastuzumab light chain 9606
36 4KMT 1 L light chain O12/KAPPA Fab 9606
37 4XTR 3 D, F Antibody Light chain 32630
38 1RZ7 1 L Fab 48d light chain 9606
39 3PGF 3 L SAB Light Chain 9606
40 2QQN 3 L Antibody light chain 9606
41 5CZX 3 D, L 20358 Fab light chain 9606
42 6BI0 2 L, M Trastuzumab anti-HER2 Fab Light Chain 9606
43 3GRW 2 L Fab light chain 9606
44 6B3K 2 L Light chain of Fab BL3-6 10090
45 6AYZ 2 C, D Fab Light Chain 9606
46 4LKC 1 A Fab fragment of PCSK9 antibody 9606
47 4KZD 2 L BL3-6 Fab antibody, light chain 10090
48 4XH2 2 B, D, F, I, K, L Fab Light Chain 9606
49 6EMJ 2 B, L fAb light chain 9606
50 3PNW 1 A, D, G, J, M, P, S, V FAB light chain 32630
51 4NRX 3 B, E, L m66 Light Chain 9606
52 3HI6 3 L, Y light chain of Fab fragment of AL-57 against alpha L I domain 9606
53 4ZFG 3 L Fragment antigen binding 5A12 light chain 9606
54 2R0L 1 L antibody light chain 32630
55 5BK1 2 D, L Synthetic antibody, Fab fragment, Light Chain 9606
56 5GGU 2 B, L light chain 9606
57 3BN9 2 C, E E2 Fab Light Chain 9606
58 3L95 1 A, L anti-NRR1 fab fragment light chain 9606
59 4KZE 2 L BL3-6 Fab antibody, light chain 10090
60 4XVU 3 D, F, J, L Antibody light chain 32630
61 3NAB 1 L Fab15 Mut6 light chain 9606
62 4Q9Q 2 L Fab BL3-6, LIGHT CHAIN 10090
63 4WV1 3 A, D Fab light chain 9606
64 5EII 2 B, L Fab Light Chain 9606
65 4UB0 2 L IgG1, light chain 9606
66 1FVD 1 A, C IGG1-KAPPA 4D5 FAB (LIGHT CHAIN) 9606
67 1BJ1 1 J, L FAB FRAGMENT HUMANIZED VERSION OF A MONOCLONAL MURINE ANTI-VEGF ANTIBODY 10090
68 4K94 1 L Fab19 heavy chain 9606
69 5VEB 2 B, L anti-CDH6 Fab light chain 9606
70 5E08 2 L Fab Light Chain 9606
71 6AZ2 3 E, F Fab Light Chain 9606
72 1CZ8 2 L, X LIGHT CHAIN OF NEUTRALIZING ANTIBODY MUTATED FORM OF A HUMANIZED MURINE ANTIBODY LIGHT CHAIN 10090
73 4XAK 3 E, L Light chain of neutralizing antibody m336 9606
74 4EDW 2 L tanezumab Fab light chain 9606
75 1FVE 1 A, C IGG1-KAPPA 4D5 FAB (LIGHT CHAIN) 9606
76 2H9G 1 A, L Fab BdF1, light chain Fab fragment 9606
77 4G7V 2 L fragment antibody light chain 9606
78 5EU7 3 C, D FAB light chain 9606
79 3FZU 1 D, L immunoglobulin IgG1 Fab, light chain 9606
80 3K2U 4 L Antibody, Fab fragment, Light Chain 9606
81 5VSH 2 B, D, F, L CH1/Clambda Fab light chain 9606
82 2HFG 1 L CB3s Fab light chain (kappa) 9606
83 3JWD 3 L, O FAB 48D LIGHT CHAIN 9606
84 4JQI 3 L Fab30 light chain 10090
85 3U30 2 B, E Light chain Fab 9606
86 5I15 1 L FAB LIGHT CHAIN 9606
87 2FJF 1 A, C, E, G, J, L, M, O, Q, S, U, W Light Chain of a VEGF binding Antibody 9606
88 5I1E 1 L FAB LIGHT CHAIN 9606
89 2QQK 3 L Antibody Light Chain 9606
90 4RRP 1 A, B, C, D, E, F Fab antibody, light chain 9606
91 4XGZ 2 B, D, F, I, K, L, N, P, R, T, V, X FAB LIGHT CHAIN 9606
92 1N8Z 1 A Herceptin Fab (antibody) - light chain 10090
93 5BK2 3 D, L sAB Light Chain 9606
94 1TZH 2 A, L Fab YADS1 Light Chain 10090
95 5BO1 3 L, M Fab light chain 9606
96 4M6O 1 L CNTO7309 light chain 9606
97 4DVR 2 L Fab 48d Light chain 9606
98 4XWO 3 D, F, J, L, P, R, V, X Antibody light chain 32630
99 4ZFF 2 B, L Fragment antigen binding (Fab) 5A12 Light chain 9606
100 3HI5 2 L light chain of Fab fragment of AL-57 against alpha L I domain 9606
101 3DVG 1 A Human IgG1 fab fragment light chain 9606
102 2FGW 1 L H52 FAB (LIGHT CHAIN) 9606
103 2FJG 2 A, L Fab light chain 9606
104 4DKF 3 L, M FAb2 Light Chain 9606
105 1HEZ 1 A, C KAPPA LIGHT CHAIN OF IG 1-214 9606
106 3EFD 1 L FabL 10090
107 4LF3 1 A, D Fab heavy chain 10090
108 5K59 4 F, L Fab light chain 9606
109 5F3H 2 B, D, F, H humanized RK35 antibody light chain 10090
110 4G7Y 2 L Fragment antibody light chain 9606
111 4PY8 4 J antibody 3.1 light chain Fab 9606
112 3DVN 1 A, L Human IgG1 fab fragment light chain 9606
113 3UC0 3 L, M Light chain, monoclonal antibody 5H2 Fab 9598
114 4NNP 3 L, Y Light chain of antagonistic fab fragment 9606
115 4ERS 1 L Fab light chain 9606
116 1DEE 1 A, C, E IGM RF 2A2 FAB LIGHT CHAIN 9606
117 2WUC 5 L FAB FRAGMENT FAB40.DELTATRP LIGHT CHAIN 9606
118 4PY7 2 B, J antibody 3.1 light chain Fab 9606
119 4K8R 3 C Fab1, light chain 9606
120 1TZI 1 A Fab YADS2 Light Chain 10090
121 4YK4 1 B, Y 641 I-9 VLCL antibody 9606
122 3R1G 3 L FAB of YW412.8.31 antibody light chain 9606
123 2QQL 3 L Antibody Light Chain 9606
124 4MXV 2 E, L, X anti-Lymphotoxin alpha antibody light chain Fab 9606
125 3WD5 2 L Adalimumab Light Chain 9606
126 5GZO 3 D, L Antibody light chain 9606
127 2WUB 4 L, Q FAB FRAGMENT FAB40.DELTATRP LIGHT CHAIN 9606
128 2FJH 2 A, L Fab fragment light chain 9606
129 5XEZ 3 D, L Antibody, mAb1, light chain 9606
130 4K9E 1 L light chain 10090
131 3P0V 1 L, M Fab DL11 light chain 9606
132 3HMX 3 L USTEKINUMAB FAB LIGHT CHAIN 9606
133 5WUX 2 B, D, L light 9606
134 4I18 1 B, L antibody light chain Fab 10090
135 4Q9R 2 L Fab BL3-6, LIGHT CHAIN 10090
136 3IVK 1 B, L Fab light chain man 10090
137 5I19 1 L FAB LIGHT CHAIN 9606
138 5X8L 2 K, L, M, N, O atezolizumab light chain 9606
139 1RZI 1 A, C, E, G, I, K, M, O Fab 47e light chain 9606
140 2R56 2 L, M IgE Fab Fragment, light chain 9606
141 5CZV 3 L Fab 20350 light chain 9606
142 5XF1 3 D, L Antibody mAb1 Light chain 9606
143 4P59 3 L MOR09825 Fab fragment light chain 9606
144 5XXY 2 L light chain of atezolizumab fab 9606
145 5CJO 3 L FAB light chain 10090
146 3N85 2 L Fab37 Light Chain 9606
147 3G6J 3 E, G Fab light chain 9606
148 3HMW 1 L USTEKINUMAB FAB LIGHT CHAIN 9606
149 4DKE 3 L, M FAb1.1 Light Chain 9606
150 4NRY 1 B, L m66 Heavy Chain 9606
151 5XHF 1 A, C polypeptide (L chain) 10090
152 5VL7 4 L Fab33 light chain 9606
153 1S78 2 C, E Pertuzumab Fab light chain 10090
154 4NYL 1 B, D, F, L Adalimumab Light Chain 9606
155 5D1Q 1 A D2-06 Light Chain 9606
156 1ZA3 1 A, L Fab-YSd1 light chain Fab light chain 9606
157 3UAJ 3 D, L Light chain, monoclonal antibody 5H2 Fab 9598
158 4IOF 3 D, F Fab-bound IDE, light chain 10090
159 4M1C 3 D, F Fab-bound IDE, light chain 9606
160 2JIX 1 A, G, L ABT-007 FAB FRAGMENT 9606
161 3ULV 2 L Fab15 light chain 9606
162 4MXW 5 L, V anti-Lymphotoxin alpha antibody light chain Fab 9606
163 5UOE 3 L, N, Q, T, W FAB light chain 9606
164 5JW3 4 L MEDI8852 light chain 9606
165 5CWS 1 A, G sAB-158 Fab Light Chain 9606
166 2R0K 2 L antibody light chain of Fab58 9606
167 5C8J 2 B, D, F, H Antibody fragment, light chain OBTAINED BY PHAGE DISPLAY FROM A LIBRARY OF HUMAN IGG. ANTIBODY FRAGMENT; THE CDRS ARE COMPLETELY SYNTHETIC 9606
168 4G80 3 B, D, F, H fragment antibody light chain 9606
169 3JWO 3 L FAB 48D LIGHT CHAIN 9606
170 3P11 2 L Fab DL11 light chain 9606
171 3ULU 2 L Fab15 light chain 9606
172 4XI5 3 C Fab-94 light chain 9606
173 4Q5Z 3 J, L, N, P, R, T, V, X IDE-bound Fab, light chain 10090
174 5JW4 4 N, P, T, V, X MEDI8852 light chain 9606
175 5JW4 6 R MEDI8852 light chain 9606
176 2QR0 1 A, E, G, K, M, Q, S, W Fab-Fragment Light Chain 9606
177 3EFF 1 A, C FAB 10090
178 3PJS 1 A, C FAB light chain 10090
179 5DWU 4 L Fab - Light Chain 9606
180 4XMN 6 L Antibody 87 light chain 32630
181 4XMM 8 L Antibody 57 light chain 9606
182 6BF7 3 D, F Fab H11-E light chain 10090
183 6BF9 3 D, F Fab H11-E light chain 10090
184 6B7Z 3 D, F FAB H11 light chain 10090
185 6B70 3 D, F FAB H11-E light chain 10090
186 3J70 2 B, N, S monoclonal antibody 17b heavy chain 9606
187 3CM9 3 L, M, N, O Ig alpha-2 chain C region 9606
188 3CHN 1 L, M, N, O Immunoglobulin kappa light chain 9606
189 2QTJ 1 L, M, N, O Kappa light chain IgA1 9606
190 2ESG 1 L, M Immunoglobulin A1 light chain 9606
191 1R70 1 A, C Human IgA2(m1) Light Chain 9606
192 1IGA 2 C, D IGA1 CHAINS A AND B, HEAVY, CHAINS C AND D, LIGHT 9606