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 34107
95 % 1 2 21880 Flexibility: Low
Max RMSD: 0.6, Avg RMSD: 0.6
PDBFlex
90 % 1 2 21261
70 % 69 127 181
50 % 69 127 226
40 % 69 127 245
30 % 69 130 249
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 38 711
95 % 20 43 845 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 1.2
PDBFlex
90 % 20 43 877
70 % 20 43 908
50 % 20 43 956
40 % 20 43 982
30 % 20 43 955
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 15377
95 % 68 170 67 Flexibility: Low
Max RMSD: 6.5, Avg RMSD: 2.2
PDBFlex
90 % 393 721 3
70 % 1269 2329 1
50 % 2593 4717 1
40 % 2593 4717 1
30 % 2976 5571 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 15316
95 % 2 5 9295 Flexibility: Low
Max RMSD: 1.4, Avg RMSD: 1.0
PDBFlex
90 % 2 5 9197
70 % 1258 2282 2
50 % 2594 4717 1
40 % 2594 4717 1
30 % 2977 5571 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.


ACTION - (A) Select for download / view details OR (B) Select two chains for comparison
Rank PDB ID Entity ID Chains Description Details Taxonomy EC Number
1 4JZZ 1 A HIV-1 YU2 gp120 glycoprotein 11676
2 4J6R 1 G Envelope glycoprotein gp160 11676
3 4XVT 1 G ENVELOPE GLYCOPROTEIN GP120 OF HIV-1 CLADE A/E 11676
4 4JZW 1 A, G HIV-1 YU2 gp120 glycoprotein 11676
5 4XMP 1 G Envelope glycoprotein gp160,Envelope glycoprotein gp160,Envelope glycoprotein gp160 UNP RESIDUES 43-122, 195-297, 319-481 11676
6 4KA2 1 A HIV-1 YU2 gp120 11676
7 4YDL 1 A, G Envelope glycoprotein gp160,Envelope glycoprotein gp160 UNP residues 43-122, 201-303, 325-486 11676
8 4DKR 1 A, C HIV-1 gp120 core 11676
9 4H8W 1 G HIV-1 CLADE A/E 93TH057 (H375S) GP120 9606
10 4DKP 1 A, C clade A/E 93TH057 HIV-1 gp120 core 11676
11 3SE8 1 G HIV-1 Clade AE strain 93TH057 gp120 Core gp120 with truncations 11676
12 4DKQ 1 A clade A/E 93TH057 HIV-1 gp120 core 11676
13 3TGT 1 A HIV-1 clade A/E 93TH057 gp120 11676
14 5F9O 1 G clade A/E 93TH057 HIV-1 gp120 core 11676
15 4DVV 1 A, B clade A/E 93TH057 HIV-1 gp120 core 11676
16 4XVS 3 G Donor 45 01dG5 coreE gp120 11676
17 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
18 2NXY 1 A ENVELOPE GLYCOPROTEIN GP120 CORE 11676
19 3SE9 1 G HIV-1 Clade AE strain 93TH057 gp120 Core gp120 with trancations 11676
20 2NY2 1 A ENVELOPE GLYCOPROTEIN GP120 CORE 11676
21 4DKO 1 A, C HIV-1 gp120 core 11676
22 4RZ8 1 A, B, C, D Envelope glycoprotein gp120 UNP residues 43-122, 201-303, 325-486 11676
23 2NY4 1 A ENVELOPE GLYCOPROTEIN GP120 CORE 11676
24 2NY3 1 A ENVELOPE GLYCOPROTEIN GP120 CORE 11676
25 5FA2 1 A, B gp120 9606
26 2NY1 1 A ENVELOPE GLYCOPROTEIN GP120 CORE 11676
27 4K0A 1 A HIV-1 YU2 gp120 glycoprotein 11676
28 4LSP 1 G HIV-1 CLADE A/E STRAIN 93TH057 GP120 11676
29 5U6E 1 A, B clade A/E 93TH057 HIV-1 gp120 core clade A/E 93TH057 HIV-1 gp120 core, V1/V2 and V3 region deletion, H375S 11676
30 2NXZ 1 A ENVELOPE GLYCOPROTEIN GP120 CORE 11676
31 4DVS 1 A, B clade A/E 93TH057 HIV-1 gp120 core 11676
32 4LAJ 1 A, B, F, J HIV-1 YU2 gp120 envelope glycoprotein 11676
33 4OM1 1 G Envelope glycoprotein gp160 UNP RESIDUES 43-122, 201-303, 325-486 11676
34 5TE7 3 G HIV-1 gp120 core 11676
35 4OLZ 1 G Envelope glycoprotein gp160 UNP RESIDUES 43-122, 201-303, 325-486 11676
36 4DVW 1 A, B clade A/E 93TH057 HIV-1 gp120 core 11676
37 4DKV 1 A, B HIV-1 gp120 core Chimera residues 44-492 11676
38 5F96 1 G clade A/E 93TH057 HIV-1 gp120 core 11676
39 4LSU 1 G HIV-1 CLADE A/E STRAIN 93TH057 GP120 11676
40 4OLU 1 G Envelope glycoprotein gp160 UNP RESIDUES 43-122, 201-303, 325-486 11676
41 4OLX 1 G Envelope glycoprotein gp160 UNP RESIDUES 43-122, 201-303, 325-486 11676
42 4XNY 1 G Envelope glycoprotein gp160,Envelope glycoprotein gp160,Envelope glycoprotein gp160 UNP RESIDUES 43-122, 195-297, 319-481 11676
43 2NY0 1 A ENVELOPE GLYCOPROTEIN GP120 CORE 11676
44 4LSQ 1 G ENVELOPE GLYCOPROTEIN GP120 WITH LOOP D AND V5 FROM STRAIN 3415_V1_C1 11676
45 4RWY 1 A HIV-1 YU2 gp120 11676
46 1YYM 1 G, P Exterior membrane glycoprotein(GP120),Exterior membrane glycoprotein(GP120),Exterior membrane glycoprotein(GP120) UNP residues 82-126,UNP residues 191-293,UNP residues 325-479 11676
47 4OM0 1 G Envelope glycoprotein gp160 UNP RESIDUES 43-122, 201-303, 325-486 11676
48 4LSR 1 G ENVELOPE GLYCOPROTEIN GP120 WITH LOOP D AND V5 FROM STRAIN ker_2018_11 11676
49 2I5Y 1 G, P Exterior membrane glycoprotein(GP120) CORE 12721
50 2NY7 1 G ENVELOPE GLYCOPROTEIN GP120 CORE 11676
51 4OLY 1 G Envelope glycoprotein gp160 UNP RESIDUES 43-122, 201-303, 325-486 11676
52 3IDX 1 G HIV-1 HxBc2 gp120 core 11676
53 4DVT 1 A, B clade A/E 93TH057 HIV-1 gp120 core 11676
54 4DVX 1 A, B clade A/E 93TH057 HIV-1 gp120 core 11676
55 4YDJ 1 G, I Envelope glycoprotein gp160,Envelope glycoprotein gp160 UNP residues 43-122, 201-303, 325-486 11676
56 2I60 1 G, P EXTERIOR MEMBRANE GLYCOPROTEIN(GP120) CORE 11676
57 4I54 1 A, B HIV-1 glycoprotein 11676
58 2NY5 1 G ENVELOPE GLYCOPROTEIN GP120 CORE 11676
59 4LST 1 G ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C 11676
60 3U7Y 2 G Envelope glycoprotein gp160 gp120 core (UNP RESIDUES 43-122, 201-303, 325-486) 11676
61 4DKU 1 A, B HIV-1 gp120 core Chimera residue 44-492 11676
62 4S1Q 1 G HIV-1 gp120 core residue 44-492 11676
63 4OLV 1 G Envelope glycoprotein gp160 UNP RESIDUES 43-122, 201-303, 325-486 11676
64 1RZJ 1 G ENVELOPE GLYCOPROTEIN GP120 part of Envelope polyprotein GP160 CORE 11676
65 4LSS 1 G envelope glycoprotein GP120 11676
66 1GC1 1 G ENVELOPE PROTEIN GP120 CORE 11676
67 5TE6 1 G clade A/E 93TH057 HIV-1 gp120 core 11676
68 1G9M 1 G ENVELOPE GLYCOPROTEIN GP120 CORE 11676
69 3JWD 1 A, B HIV-1 GP120 ENVELOPE GLYCOPROTEIN 11676
70 4YE4 1 G HT593.1 gp120 HIV-1 clade B gp120 core 12721
71 3NGB 1 A, D, G, I Envelope glycoprotein gp160 UNP RESIDUES 43-122, 201-303, 325-486 11676
72 4OLW 1 G Envelope glycoprotein gp160 UNP RESIDUES 43-122, 201-303, 325-486 11676
73 4DVR 1 G Envelope glycoprotein gp120 unp residues 82-122; 199-297; 319-479 11676
74 5F9W 1 A, G clade A/E 93TH057 HIV-1 gp120 core 11676
75 1YYL 1 G, P Exterior membrane glycoprotein(GP120),Exterior membrane glycoprotein(GP120),Exterior membrane glycoprotein(GP120) UNP residues 82-126,UNP residues 191-293,UNP residues 325-479 11676
76 2NY6 1 A ENVELOPE GLYCOPROTEIN GP120 CORE 11676
77 4JKP 1 G gp120 11676
78 5TE4 1 G HIV-1 clade G strain X2088 gp120 Extended core portion of HIV-1 gp120 11676
79 4JPV 1 G HIV-1 CLADE A STRAIN 93TH057 GP120 WITH LOOP d AND LOOPD V5 REPLACED FROM HIV STRAIN 3415V1 11676
80 4I53 1 A, B HIV-1 glycoprotein 11676
81 3HI1 1 G, J Glycoprotein 120 11676
82 1RZK 1 G ENVELOPE GLYCOPROTEIN GP120 part of Envelope polyprotein GP160 CORE 11676
83 1G9N 1 G ENVELOPE GLYCOPROTEIN GP120 CORE 11676
84 4JPW 1 G HIV-1 CLADE A/E STRAIN 73TH057 GP120 WITH MUTATION H375S 11676
85 4JB9 1 G clade A/E 93TH057 HIV-1 gp120 core 11676
86 3TGR 1 A, B HIV-1 clade C1086 gp120 11676
87 3TGS 1 A, B HIV-1 clade C1086 gp120 core 11676
88 3RJQ 1 A C186 gp120 11676
89 5F4L 1 A, B ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C 11676
90 4JAN 1 G, I ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C 11676
91 3IDY 1 A, G HIV-1 HxBc2 gp120 core 11676
92 5FEC 3 C, D, G, I 426c.TM4deltaV1-3 gp120 11676
93 5F4P 1 A, D ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C 11676
94 5W4L 1 A, G clade A/E 93TH057 HIV-1 gp120 core 11676
95 5F4U 1 A, B ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C 11676
96 2QAD 1 A, E Envelope glycoprotein gp160 CORE WITH V3 11676
97 5F4R 1 A, C ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C 11676
98 4P9H 2 G Envelope glycoprotein gp160 GP120 CORE, (UNP RESIDUES 43-122, 201-303, 325-486) 11676
99 4R2G 1 A, E, K, O Surface protein gp160 11676
100 4RFO 1 G HIV-1 clade A/E gp120 11676
101 5KJR 1 G clade A/E 93TH057 HIV-1 gp120 core 11676
102 4JM2 5 E gp120 core with mini V3 loop 11676
103 5I9Q 1 A, G 426c.TM4dV1-3 p120 11676
104 5T33 3 G RHPA gp120 core 12721
105 4RX4 1 E, G HIV-1 Clade A Q842.d12 gp120 11676
106 4JDT 1 G gp120 GP120 CORE 11676
107 4LSV 1 G envelope glycoprotein GP120 11676
108 4YDI 1 G Envelope glycoprotein gp160 UNP residues 43-122, 191-293, 315-482 11676
109 3LQA 2 G Envelope glycoprotein gp160 11676
110 4S1R 1 G clade A/E 93TH057 HIV-1 gp120 core residue 44-492 11676
111 4XNZ 1 A, D, G Envelope glycoprotein gp160,Envelope glycoprotein gp160 UNP RESIDUES 43-122, 201-303, 325-486 11676
112 4RFN 1 A, G HIV-1 CLADE A/E 93TH057 (H375S) GP120 11676
113 4S1S 1 G clade A/E 93TH057 HIV-1 gp120 core residue 44-492 11676
114 4R4F 1 A HIV-1 Env gp120 11676
115 3JWO 1 A HIV-1 GP120 ENVELOPE GLYCOPROTEIN 9606
116 5CD5 1 A 93TH057 HIV-1 gp120 core 11676
117 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
118 5IGX 1 G 426c.TM1deltaV1-3 gp120 11676
119 3TGQ 1 A, B, C, D HIV-1 YU2 gp120 11676
120 2B4C 1 G envelope glycoprotein CORE with V3 11676
121 4R4N 1 A, B, E, I, M, P, S, V HIV-1 gp120 11676
122 3TIH 1 A, B, C, D HIV-1 clade C ZM109F.PB4 gp120 11676
123 4RQS 4 G HIV-1 YU2 gp120 core chimeric protein 11676
124 4R4H 1 A HIV-1 Env gp120 11676
125 5F6J 1 E, G ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C 11676
126 5A8H 1 A, G, M HIV-1 GP120 11676
127 5A7X 1 A, E, I HIV-1 YU2 GP120 11676