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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 # 287 Members. Sequence cutoff: 70% Cluster size: 71 sequences
Rank   PDB id Entity id Chains Description Details Taxonomy EC Number
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1 4JZZ 1 A HIV-1 YU2 gp120 glycoprotein 11676  
2 4J6R 1 G Envelope glycoprotein gp160 11676  
3 4JZW 1 A, G HIV-1 YU2 gp120 glycoprotein 11676  
4 4XMP 1 G Envelope glycoprotein gp160,Envelope glycoprotein gp160,Envelope glycoprotein gp160 UNP RESIDUES 43-122, 195-297, 319-481 11676  
5 4KA2 1 A HIV-1 YU2 gp120 11676  
6 4YDL 1 A, G Envelope glycoprotein gp160,Envelope glycoprotein gp160 UNP residues 43-122, 201-303, 325-486 11676  
7 4DKR 1 A, C HIV-1 gp120 core 11686  
8 4H8W 1 G HIV-1 CLADE A/E 93TH057 (H375S) GP120 9606  
9 4DKP 1 A, C clade A/E 93TH057 HIV-1 gp120 core 11686  
10 3SE8 1 G HIV-1 Clade AE strain 93TH057 gp120 Core gp120 with truncations 11676  
11 4DKQ 1 A clade A/E 93TH057 HIV-1 gp120 core 11686  
12 3TGT 1 A HIV-1 clade A/E 93TH057 gp120 11676  
13 4DVV 1 A, B Envelope glycoprotein gp160 unp residues 43-486 11676  
14 4XVS 3 G Donor 45 01dG5 coreE gp120 11676  
15 4YDK 1 G Envelope glycoprotein gp160,Envelope glycoprotein gp160 UNP residues 43-122, 201-303, 325-486,UNP residues 43-122, 201-303, 325-486,UNP residues 43-122, 201-303, 325-486 11676  
16 3SE9 1 G HIV-1 Clade AE strain 93TH057 gp120 Core gp120 with trancations 11676  
17 4DKO 1 A, C HIV-1 gp120 core 11686  
18 4K0A 1 A HIV-1 YU2 gp120 glycoprotein 11676  
19 4LSP 1 G HIV-1 CLADE A/E STRAIN 93TH057 GP120 11676  
20 4DVS 1 A, B glycoprotein gp120 unp residues 43-122, 201-303, 325-486 11676  
21 4LAJ 1 A, B, F, J HIV-1 YU2 gp120 envelope glycoprotein 11676  
22 4OM1 1 G Envelope glycoprotein gp160 UNP RESIDUES 43-122, 201-303, 325-486 11676  
23 4OLZ 1 G Envelope glycoprotein gp160 UNP RESIDUES 43-122, 201-303, 325-486 11676  
24 4DVW 1 A, B Envelope glycoprotein gp160 unp residues 43-486 11676  
25 4DKV 1 A, B HIV-1 gp120 core Chimera residues 44-492 11676  
26 4LSU 1 G HIV-1 CLADE A/E STRAIN 93TH057 GP120 11676  
27 4OLU 1 G Envelope glycoprotein gp160 UNP RESIDUES 43-122, 201-303, 325-486 11676  
28 4OLX 1 G Envelope glycoprotein gp160 UNP RESIDUES 43-122, 201-303, 325-486 11676  
29 4XNY 1 G Envelope glycoprotein gp160,Envelope glycoprotein gp160,Envelope glycoprotein gp160 UNP RESIDUES 43-122, 195-297, 319-481 11676  
30 4LSQ 1 G ENVELOPE GLYCOPROTEIN GP120 WITH LOOP D AND V5 FROM STRAIN 3415_V1_C1 11676  
31 4RWY 1 A HIV-1 YU2 gp120 11676  
32 4OM0 1 G Envelope glycoprotein gp160 UNP RESIDUES 43-122, 201-303, 325-486 11676  
33 4LSR 1 G ENVELOPE GLYCOPROTEIN GP120 WITH LOOP D AND V5 FROM STRAIN ker_2018_11 11676  
34 4OLY 1 G Envelope glycoprotein gp160 UNP RESIDUES 43-122, 201-303, 325-486 11676  
35 4DVT 1 A, B Envelope glycoprotein gp160 unp residues 43-122, 201-303, 325-486 11676  
36 4DVX 1 A, B Envelope glycoprotein gp160 unp residues 43-486 11676  
37 4YDJ 1 G, I Envelope glycoprotein gp160,Envelope glycoprotein gp160 UNP residues 43-122, 201-303, 325-486 11676  
38 4I54 1 A, B HIV-1 glycoprotein 11676  
39 4LST 1 G ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C 11676  
40 3U7Y 2 G Envelope glycoprotein gp160 gp120 core (UNP RESIDUES 43-122, 201-303, 325-486) 11676  
41 4DKU 1 A, B HIV-1 gp120 core Chimera residue 44-492 11676  
42 4S1Q 1 G HIV-1 gp120 core residue 44-492 9606  
43 4OLV 1 G Envelope glycoprotein gp160 UNP RESIDUES 43-122, 201-303, 325-486 11676  
44 4LSS 1 G envelope glycoprotein GP120 11676  
45 3JWD 1 A, B HIV-1 GP120 ENVELOPE GLYCOPROTEIN 11676  
46 3NGB 1 A, D, G, I Envelope glycoprotein gp160 UNP RESIDUES 43-122, 201-303, 325-486 11676  
47 4OLW 1 G Envelope glycoprotein gp160 UNP RESIDUES 43-122, 201-303, 325-486 11676  
48 4JKP 1 G gp120 11676  
49 4JPV 1 G HIV-1 CLADE A STRAIN 93TH057 GP120 WITH LOOP d AND LOOPD V5 REPLACED FROM HIV STRAIN 3415V1 11676  
50 4I53 1 A, B HIV-1 glycoprotein 11676  
51 4JPW 1 G HIV-1 CLADE A/E STRAIN 73TH057 GP120 WITH MUTATION H375S 11676  
52 4JB9 1 G clade A/E 93TH057 HIV-1 gp120 core 11676  
53 3TGR 1 A, B HIV-1 clade C1086 gp120 11676  
54 3TGS 1 A, B HIV-1 clade C1086 gp120 core 11676  
55 3RJQ 1 A C186 gp120 11706  
56 4JAN 1 G, I ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C 11676  
57 4P9H 2 G Envelope glycoprotein gp120 GP120 CORE, (UNP RESIDUES 43-122, 201-303, 325-486) 11676  
58 4RX4 1 E, G HIV-1 Clade A Q842.d12 gp120 11676  
59 4JDT 1 G gp120 GP120 CORE 11676  
60 4LSV 1 G envelope glycoprotein GP120 11676  
61 4YDI 1 G Envelope glycoprotein gp160 UNP residues 43-122, 191-293, 315-482 11676  
62 4S1R 1 G clade A/E 93TH057 HIV-1 gp120 core residue 44-492 11676  
63 4XNZ 1 A, D, G Envelope glycoprotein gp160,Envelope glycoprotein gp160 UNP RESIDUES 43-122, 201-303, 325-486 11676  
64 4S1S 1 G clade A/E 93TH057 HIV-1 gp120 core residue 44-492 11676  
65 4R4F 1 A HIV-1 Env gp120 11676  
66 3JWO 1 A HIV-1 GP120 ENVELOPE GLYCOPROTEIN 9606  
67 4YFL 1 E, G Envelope glycoprotein gp160,Envelope glycoprotein gp160,Envelope glycoprotein gp160 UNP RESIDUES 43-122, 201-303, 325-486,UNP RESIDUES 43-122, 201-303, 325-486,UNP RESIDUES 43-122, 201-303, 325-486 11676  
68 3TGQ 1 A, B, C, D HIV-1 YU2 gp120 11676  
69 4R4N 1 A, B, E, I, M, P, S, V HIV-1 gp120 11676  
70 3TIH 1 A, B, C, D HIV-1 clade C ZM109F.PB4 gp120 11676  
71 4R4H 1 A HIV-1 Env gp120 11676  
 
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 26972
95% 1 2 17431
90% 1 2 16994
70% 45 71 287
50% 45 71 312
40% 45 71 343
30% 45 71 352
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 30 866
95% 20 35 984
90% 20 35 1005
70% 20 35 1036
50% 20 35 1081
40% 20 35 1102
30% 20 35 1077
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 12068
95% 45 120 71
90% 225 418 4
70% 786 1412 3
50% 1884 3355 1
40% 1885 3356 1
30% 2133 3971 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 12024
95% 2 4 11439
90% 2 4 11265
70% 917 1622 2
50% 1885 3355 1
40% 1886 3356 1
30% 2134 3971 1
 

Documentation

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