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Structure of HIV-1 gp120 with gp41-Interactive Region: Layered Architecture and Basis of Conformational Mobility
Sequence Clustering and Redundancy Reduction Results
3JWD
Cluster # 83 Members. Sequence cutoff: 95% Cluster size: 113 sequences
Rank   PDB id Entity id Chains Description Details Taxonomy EC Number
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1 3HC4 2 L IMMUNOGLOBULIN IGG1 FAB, LIGHT CHAIN 9606  
2 3NCJ 1 L Fab15 Mut8 light chain 9606  
3 3HC3 2 L IMMUNOGLOBULIN IGG1 FAB, HEAVY CHAIN 9606  
4 3NA9 1 L Fab15 light chain 9606  
5 3NAA 1 L Fab15 Mut5 light chain 9606  
6 3P0Y 3 L Fab DL11 light chain 9606  
7 3NAC 1 L Fab15 Mut7 light chain 9606  
8 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  
9 3SOB 1 L antibody light chain 9606  
10 4KQ3 1 L CNTO3186 light chain Fab 9606  
11 3HC0 2 B, L IMMUNOGLOBULIN IGG1 FAB, HEAVY CHAIN 9606  
12 2HFF 1 A, L CB2 Fab, light chain 9606  
13 1VGE 1 L TR1.9 FAB FAB FRAGMENT OF A HUMAN IGG1 KAPPA AUTOANTIBODY 9606  
14 2R8S 2 L Fab light chain 10090  
15 4HKZ 1 A Trastuzumab light chain 9606  
16 4KMT 1 L light chain O12/KAPPA Fab 9606  
17 4XTR 3 D, F Antibody Light chain 32630  
18 1RZ7 1 L Fab 48d light chain 9606  
19 3PGF 3 L SAB Light Chain 9606  
20 2QQN 3 L Antibody light chain 9606  
21 3GRW 2 L Fab light chain 9606  
22 4LKC 1 A Fab fragment of PCSK9 antibody 9606  
23 4KZD 2 L BL3-6 Fab antibody, light chain 10090  
24 3PNW 1 A, D, G, J, M, P, S, V FAB light chain 32630  
25 4NRX 3 B, E, L m66 Light Chain 9606  
26 3HI6 3 L, Y light chain of Fab fragment of AL-57 against alpha L I domain 9606  
27 2R0L 1 L antibody light chain 32630  
28 3BN9 2 C, E E2 Fab Light Chain 9606  
29 3L95 1 A, L anti-NRR1 fab fragment light chain 9606  
30 4KZE 2 L BL3-6 Fab antibody, light chain 10090  
31 4XVU 3 D, F, J, L Antibody light chain 32630  
32 3NAB 1 L Fab15 Mut6 light chain 9606  
33 1FVD 1 A, C IGG1-KAPPA 4D5 FAB (LIGHT CHAIN) 9606  
34 1BJ1 1 J, L FAB FRAGMENT HUMANIZED VERSION OF A MONOCLONAL MURINE ANTI-VEGF ANTIBODY 10090  
35 4K94 1 L Fab19 heavy chain 9606  
36 1CZ8 2 L, X LIGHT CHAIN OF NEUTRALIZING ANTIBODY MUTATED FORM OF A HUMANIZED MURINE ANTIBODY LIGHT CHAIN FAB FRAGMENT 10090  
37 1FVE 1 A, C IGG1-KAPPA 4D5 FAB (LIGHT CHAIN) 9606  
38 2H9G 1 A, L Fab BdF1, light chain Fab fragment 9606  
39 4G7V 2 L fragment antibody light chain 9606  
40 3FZU 1 D, L immunoglobulin IgG1 Fab, light chain 9606  
41 3K2U 4 L Antibody, Fab fragment, Light Chain 9606  
42 2HFG 1 L CB3s Fab light chain (kappa) 9606  
43 3JWD 3 L, O FAB 48D LIGHT CHAIN 9606  
44 4JQI 3 L Fab30 light chain 10090  
45 3U30 2 B, E Light chain Fab 9606  
46 2FJF 1 A, C, E, G, J, L, M, O, Q, S, U, W Light Chain of a VEGF binding Antibody 9606  
47 2QQK 3 L Antibody Light Chain 9606  
48 4RRP 1 A, B, C, D, E, F Fab antibody, light chain 4606  
49 1N8Z 1 A Herceptin Fab (antibody) - light chain 10090  
50 1TZH 2 A, L Fab YADS1 Light Chain 10090  
51 4M6O 1 L CNTO7309 light chain 9606  
52 4DVR 2 L Fab 48d Light chain 9606  
53 4XWO 3 D, F, J, L, P, R, V, X Antibody light chain 32630  
54 3HI5 2 L light chain of Fab fragment of AL-57 against alpha L I domain 9606  
55 3DVG 1 A Human IgG1 fab fragment light chain 9606  
56 2FGW 1 L H52 FAB (LIGHT CHAIN) 9606  
57 2FJG 2 A, L Fab light chain 9606  
58 4DKF 3 L, M FAb2 Light Chain 9606  
59 1HEZ 1 A, C KAPPA LIGHT CHAIN OF IG 1-214 9606  
60 3EFD 1 L FabL 10090  
61 4G7Y 2 L Fragment antibody light chain 9606  
62 4PY8 4 J antibody 3.1 light chain Fab 9606  
63 3DVN 1 A, L Human IgG1 fab fragment light chain 9606  
64 3UC0 3 L, M Light chain, monoclonal antibody 5H2 Fab 9598  
65 4NNP 3 L, Y Light chain of antagonistic fab fragment 9606  
66 1DEE 1 A, C, E IGM RF 2A2 FAB LIGHT CHAIN 9606  
67 2WUC 5 L FAB FRAGMENT FAB40.DELTATRP LIGHT CHAIN 9606  
68 4PY7 2 B, J antibody 3.1 light chain Fab 9606  
69 4K8R 3 C Fab1, light chain 9606  
70 1TZI 1 A Fab YADS2 Light Chain 10090  
71 3R1G 3 L FAB of YW412.8.31 antibody light chain 9606  
72 2QQL 3 L Antibody Light Chain 9606  
73 4MXV 2 E, L, X anti-Lymphotoxin alpha antibody light chain Fab 9606  
74 3WD5 2 L Adalimumab Light Chain 9606  
75 2WUB 4 L, Q FAB FRAGMENT FAB40.DELTATRP LIGHT CHAIN 9606  
76 2FJH 2 A, L Fab fragment light chain 9606  
77 4K9E 1 L light chain 10090  
78 3P0V 1 L, M Fab DL11 light chain 9606  
79 3HMX 3 L USTEKINUMAB FAB LIGHT CHAIN 9606  
80 4I18 1 B, L antibody light chain Fab 10090  
81 3IVK 1 B, L Fab light chain man 10090  
82 1RZI 1 A, C, E, G, I, K, M, O Fab 47e light chain 9606  
83 2R56 2 L, M IgE Fab Fragment, light chain 9606  
84 4P59 3 L MOR09825 Fab fragment light chain 9606  
85 3N85 2 L Fab37 Light Chain 9606  
86 3G6J 3 E, G Fab light chain 9606  
87 3HMW 1 L USTEKINUMAB FAB LIGHT CHAIN 9606  
88 4DKE 3 L, M FAb1.1 Light Chain 9606  
89 4NRY 1 B, L m66 Heavy Chain 9606  
90 1S78 2 C, E Pertuzumab Fab light chain 10090  
91 4NYL 1 B, D, F, L Adalimumab Light Chain 9606  
92 1ZA3 1 A, L Fab-YSd1 light chain Fab light chain 9606  
93 3UAJ 3 D, L Light chain, monoclonal antibody 5H2 Fab 9598  
94 4IOF 3 D, F Fab-bound IDE, light chain 10090  
95 4M1C 3 D, F Fab-bound IDE, light chain 9606  
96 3ULV 2 L Fab15 light chain 9606  
97 4MXW 5 L, V anti-Lymphotoxin alpha antibody light chain Fab 9606  
98 2R0K 2 L antibody light chain of Fab58 9606  
99 4G80 3 B, D, F, H fragment antibody light chain 9606  
100 3JWO 3 L FAB 48D LIGHT CHAIN 9606  
101 3P11 2 L Fab DL11 light chain 9606  
102 3ULU 2 L Fab15 light chain 9606  
103 2QR0 1 A, E, G, K, M, Q, S, W Fab-Fragment Light Chain 9606  
104 3EFF 1 A, C FAB 10090  
105 3PJS 1 A, C FAB light chain 10090  
106 4XMN 6 L Antibody 87 light chain 32630  
107 4XMM 8 L Antibody 57 light chain 9606  
108 3CM9 3 L, M, N, O Ig alpha-2 chain C region 9606  
109 3CHN 1 L, M, N, O Immunoglobulin kappa light chain 9606  
110 2QTJ 1 L, M, N, O Kappa light chain IgA1 9606  
111 2ESG 1 L, M Immunoglobulin A1 light chain 9606  
112 1R70 1 A, C Human IgA2(m1) Light Chain 9606  
113 1IGA 2 C, D IGA1 CHAINS A AND B, HEAVY, CHAINS C AND D, LIGHT 9606  
 
Sequence Clusters for the Sequence Entities in PDB 3JWD
Entity #1: Chains: A,B - HIV-1 GP120 ENVELOPE GLYCOPROTEIN protein, length: 379 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
100% 1 1 26334
95% 1 2 17063
90% 1 2 16627
70% 37 57 357
50% 37 57 395
40% 37 57 417
30% 37 57 424
Entity #2: Chains: C,D - T-cell surface glycoprotein CD4 protein, length: 184 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
100% 17 30 850
95% 20 35 954
90% 20 35 973
70% 20 35 1005
50% 20 35 1046
40% 20 35 1076
30% 20 35 1055
Entity #3: Chains: L,O - FAB 48D LIGHT CHAIN protein, length: 213 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
100% 2 4 11786
95% 43 113 83
90% 210 389 4
70% 761 1349 3
50% 1817 3210 1
40% 1818 3211 1
30% 2058 3793 1
Entity #4: Chains: H,P - FAB 48D HEAVY CHAIN protein, length: 220 [Blast  ]
Cluster Sequence Similarity Cutoff Rank   Nr. of chains in Cluster Cluster Nr.  
100% 2 4 11742
95% 2 4 11215
90% 2 4 11044
70% 882 1548 2
50% 1818 3210 1
40% 1819 3211 1
30% 2059 3793 1
 

Documentation

Click here for more detailed documentation on the redundancy reduction and sequence clustering procedure used by RCSB.