Sequence Similarity Clusters for the Entities in PDB 2NXZ

Entity #1 | Chains: A
ENVELOPE GLYCOPROTEIN GP120 protein, length: 317 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 4 4 22017
95 % 6 15 4552 Flexibility: Medium
Max RMSD: 16.1, Avg RMSD: 5.5
PDBFlex
90 % 6 15 4584
70 % 30 192 130
50 % 30 192 157
40 % 30 192 168
30 % 30 195 184
Entity #2 | Chains: B
T-cell surface glycoprotein CD4 protein, length: 184 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 8 40 854
95 % 8 46 804 Flexibility: Low
Max RMSD: 2.4, Avg RMSD: 1.2
PDBFlex
90 % 8 46 836
70 % 8 46 887
50 % 8 46 935
40 % 8 46 960
30 % 8 46 943
Entity #3 | Chains: C
ANTIBODY 17B, LIGHT CHAIN protein, length: 214 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 6 22 1484
95 % 8 34 1108 Flexibility: Low
Max RMSD: 5.3, Avg RMSD: 1.2
PDBFlex
90 % 244 844 2
70 % 742 2696 1
50 % 1527 5473 1
40 % 1782 6175 1
30 % 2164 7653 1
Entity #4 | Chains: D
ANTIBODY 17B, HEAVY CHAIN protein, length: 229 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 6 26 1209
95 % 6 26 1446 Flexibility: Low
Max RMSD: 3.9, Avg RMSD: 1.0
PDBFlex
90 % 6 26 1473
70 % 736 2655 2
50 % 1528 5473 1
40 % 1783 6175 1
30 % 2165 7653 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 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 6BF4 1 A, G HIV-1 clade AE gp120 core 11676
52 4OLY 1 G Envelope glycoprotein gp160 UNP RESIDUES 43-122, 201-303, 325-486 11676
53 3IDX 1 G HIV-1 HxBc2 gp120 core 11676
54 4DVT 1 A, B clade A/E 93TH057 HIV-1 gp120 core 11676
55 4DVX 1 A, B clade A/E 93TH057 HIV-1 gp120 core 11676
56 4YDJ 1 G, I Envelope glycoprotein gp160,Envelope glycoprotein gp160 UNP residues 43-122, 201-303, 325-486 11676
57 2I60 1 G, P EXTERIOR MEMBRANE GLYCOPROTEIN(GP120) CORE 11676
58 5WB9 1 G clade A/E 93TH057 HIV-1 gp120 core 11676
59 4I54 1 A, B HIV-1 glycoprotein 11676
60 2NY5 1 G ENVELOPE GLYCOPROTEIN GP120 CORE 11676
61 4LST 1 G ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C 11676
62 3U7Y 2 G Envelope glycoprotein gp160 gp120 core (UNP RESIDUES 43-122, 201-303, 325-486) 11676
63 4DKU 1 A, B HIV-1 gp120 core Chimera residue 44-492 11676
64 4S1Q 1 G HIV-1 gp120 core residue 44-492 11676
65 4OLV 1 G Envelope glycoprotein gp160 UNP RESIDUES 43-122, 201-303, 325-486 11676
66 1RZJ 1 G ENVELOPE GLYCOPROTEIN GP120 part of Envelope polyprotein GP160 CORE 11676
67 4LSS 1 G envelope glycoprotein GP120 11676
68 1GC1 1 G ENVELOPE PROTEIN GP120 CORE 11676
69 5TE6 1 G clade A/E 93TH057 HIV-1 gp120 core 11676
70 1G9M 1 G ENVELOPE GLYCOPROTEIN GP120 CORE 11676
71 6MFT 3 C, G Gp120 426c core, residues 44-494 9606
72 3JWD 1 A, B HIV-1 GP120 ENVELOPE GLYCOPROTEIN 11676
73 4YE4 1 G HT593.1 gp120 HIV-1 clade B gp120 core 12721
74 3NGB 1 A, D, G, I Envelope glycoprotein gp160 UNP RESIDUES 43-122, 201-303, 325-486 11676
75 4OLW 1 G Envelope glycoprotein gp160 UNP RESIDUES 43-122, 201-303, 325-486 11676
76 4DVR 1 G Envelope glycoprotein gp120 unp residues 82-122; 199-297; 319-479 11676
77 5F9W 1 A, G clade A/E 93TH057 HIV-1 gp120 core 11676
78 5UKR 3 G Chimeric B.YU2 gp120 core derived from HIV-1 Env 11676
79 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
80 2NY6 1 A ENVELOPE GLYCOPROTEIN GP120 CORE 11676
81 4JKP 1 G gp120 11676
82 5TE4 1 G HIV-1 clade G strain X2088 gp120 Extended core portion of HIV-1 gp120 11676
83 4JPV 1 G HIV-1 CLADE A STRAIN 93TH057 GP120 WITH LOOP d AND LOOPD V5 REPLACED FROM HIV STRAIN 3415V1 11676
84 5UEM 1 G clade A/E 93TH057 HIV-1 gp120 core 11676
85 4I53 1 A, B HIV-1 glycoprotein 11676
86 6BCK 1 G clade A/E 93TH057 HIV-1 gp120 core 11676
87 3HI1 1 G, J Glycoprotein 120 11676
88 1RZK 1 G ENVELOPE GLYCOPROTEIN GP120 part of Envelope polyprotein GP160 CORE 11676
89 1G9N 1 G ENVELOPE GLYCOPROTEIN GP120 CORE 11676
90 4JPW 1 G HIV-1 CLADE A/E STRAIN 73TH057 GP120 WITH MUTATION H375S 11676
91 4JB9 1 G clade A/E 93TH057 HIV-1 gp120 core 11676
92 3TGR 1 A, B HIV-1 clade C1086 gp120 11676
93 3TGS 1 A, B HIV-1 clade C1086 gp120 core 11676
94 3RJQ 1 A C186 gp120 11676
95 5F4L 1 A, B ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C 11676
96 4JAN 1 G, I ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C 11676
97 6CK9 4 G gp120 of Envelope glycoprotein gp160 11676
98 3IDY 1 A, G HIV-1 HxBc2 gp120 core 11676
99 5FEC 3 C, D, G, I 426c.TM4deltaV1-3 gp120 11676
100 5F4P 1 A, D ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C 11676
101 5W4L 1 A, G clade A/E 93TH057 HIV-1 gp120 core 11676
102 4TVP 1 G Envelope glycoprotein gp160 UNP residues 30-505 11676
103 5FYJ 4 G GP120 ENV ECTODOMAIN GP120 ENV ECTODOMAIN, RESIDUES 32-506 11676
104 5F4U 1 A, B ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C 11676
105 2QAD 1 A, E Envelope glycoprotein gp160 CORE WITH V3 11676
106 5F4R 1 A, C ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C 11676
107 5CAY 1 G Envelope glycoprotein gp120 core from ST strain of HIV-2 11709
108 4P9H 2 G Envelope glycoprotein gp160 GP120 CORE, (UNP RESIDUES 43-122, 201-303, 325-486) 11676
109 5CEZ 1 G Envelope glycoprotein gp160 UNP residues 31-505 11676
110 4R2G 1 A, E, K, O Surface protein gp160 11676
111 4RFO 1 G HIV-1 clade A/E gp120 11676
112 5KJR 1 G clade A/E 93TH057 HIV-1 gp120 core 11676
113 5U7M 4 G Envelope glycoprotein gp160 UNP residues 30-505 11676
114 4JM2 5 E gp120 core with mini V3 loop 11676
115 5I9Q 1 A, G 426c.TM4dV1-3 p120 11676
116 5T33 3 G RHPA gp120 core 12721
117 4RX4 1 E, G HIV-1 Clade A Q842.d12 gp120 11676
118 4JDT 1 G gp120 GP120 CORE 11676
119 5FYK 4 G JR-FL, GP120 ENV ECTODOMAIN GP120 ENV ECTODOMAIN 11676
120 4LSV 1 G envelope glycoprotein GP120 11676
121 5FYL 4 G BG505 GP120 ENV ECTODOMAIN GP120 ENV ECTODOMAIN 11676
122 5W6D 1 G BG505-SOSIP.v4.1-GT1-N137A gp120 11676
123 5UTF 1 G Envelope glycoprotein gp120 11676
124 4YDI 1 G Envelope glycoprotein gp160 UNP residues 43-122, 191-293, 315-482 11676
125 5UWE 1 G clade A/E 93TH057 HIV-1 gp120 core 11676
126 3LQA 2 G Envelope glycoprotein gp160 11676
127 5U7O 4 G Envelope glycoprotein gp160 UNP residues 30-510 11676
128 5UTY 4 G HIV-1 BG505 strain Env gp120 UNP residues 29-505 11676
129 4S1R 1 G clade A/E 93TH057 HIV-1 gp120 core residue 44-492 11676
130 4XNZ 1 A, D, G Envelope glycoprotein gp160,Envelope glycoprotein gp160 UNP RESIDUES 43-122, 201-303, 325-486 11676
131 5CJX 4 G, K, Y BG505 Env gp120 UNP residues 32-505 11676
132 4RFN 1 A, G HIV-1 CLADE A/E 93TH057 (H375S) GP120 11676
133 4ZMJ 1 G Envelope glycoprotein gp160 11676
134 4S1S 1 G clade A/E 93TH057 HIV-1 gp120 core residue 44-492 11676
135 4R4F 1 A HIV-1 Env gp120 11676
136 6CH7 4 G Envelope glycoprotein gp120 11676
137 3JWO 1 A HIV-1 GP120 ENVELOPE GLYCOPROTEIN 9606
138 5CD5 1 A 93TH057 HIV-1 gp120 core 11676
139 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
140 5IGX 1 G 426c.TM1deltaV1-3 gp120 11676
141 5V7J 1 G Envelope glycoprotein gp160 UNP residues 31-505 11676
142 3TGQ 1 A, B, C, D HIV-1 YU2 gp120 11676
143 6CH8 4 G Envelope glycoprotein gp120 11676
144 5T3Z 2 G Envelope glycoprotein gp160 UNP residues 30-508 11676
145 5UM8 1 G glycoprotein gp120 11676
146 6DE7 4 G Envelope glycoprotein gp160 11676
147 2B4C 1 G envelope glycoprotein CORE with V3 11676
148 4R4N 1 A, B, E, I, M, P, S, V HIV-1 gp120 11676
149 3TIH 1 A, B, C, D HIV-1 clade C ZM109F.PB4 gp120 11676
150 5T3X 2 G Envelope glycoprotein gp160 UNP residues 30-508 11676
151 5T3S 1 G Envelope glycoprotein gp160 11676
152 5I8H 1 A, C BG505 SOSIP.664 gp120 11676
153 4RQS 4 G HIV-1 YU2 gp120 core chimeric protein 11676
154 5D9Q 1 A, G, J Envelope glycoprotein gp120 11676
155 5C7K 3 C Envelope glycoprotein gp120 UNP Residues 30-507 11676
156 4R4H 1 A HIV-1 Env gp120 11676
157 6CH9 4 G Envelope glycoprotein gp120 11676
158 3FUS 1 A EXTERIOR MEMBRANE GLYCOPROTEIN GP120 GP120 CORE, RESIDUES 66-109, 209-311, 342-502 11723
159 6CE0 2 G Envelope glycoprotein gp160 11676
160 5F6J 1 E, G ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C 11676
161 5JSA 3 C gp120 11676
162 2BF1 1 A EXTERIOR MEMBRANE GLYCOPROTEIN GP120 GP120 CORE, RESIDUES 66-109,209-311,342-502 11723
163 5JS9 3 C gp120 11676
164 6CCB 2 C, G Glycoprotein 120 11676
165 5WDU 1 F, G, Q Envelope glycoprotein gp160 11676
166 4NCO 1 A, E, I BG505 SOSIP gp120 UNP residues 30-504 11676
167 6CHB 2 F, G, H Envelope glycoprotein gp120 11676
168 6MET 1 G Envelope glycoprotein gp160 GP120 domain residues 29-489 11676
169 6MEO 1 G Envelope glycoprotein gp160 GP120 domain residues 29-489 11676
170 6MAR 3 A, C, E Envelope glycoprotein gp160 11676
171 6EDU 2 D, E, F Envelope glycoprotein gp160 11676
172 6DID 1 A, F, G Envelope glycoprotein gp160 GP120 domain residues 30-505 11676
173 6DCQ 1 A, C, E Envelope glycoprotein gp160 GP120 domain residues 28-507 11676
174 6CUE 1 2, C, c Envelope glycoprotein gp120 11676
175 6CUF 7 2, C, d Envelope glycoprotein gp120 11676
176 6CRQ 1 A, B, F Envelope glycoprotein gp160 11676
177 6CM3 2 D, E, F Envelope glycoprotein gp160 11676
178 6CDE 8 2, C, c Glycoprotein 120 11676
179 6CDI 2 2, C, d Glycoprotein 120 11676
180 5VN3 3 G, I, J Envelope glycoprotein gp160 11676
181 5VN8 1 D, E, G Envelope glycoprotein gp160 11676
182 5VJ6 2 D, E, F Envelope glycoprotein gp160 UNP residues 30-505 11676
183 5VIY 2 D, E, F Envelope glycoprotein gp160 UNP residues 30-505 11676
184 5V8L 1 A, C, D gp120 UNP residues 30-505 11676
185 5V8M 1 A, F, G gp120 UNP residues 30-505 11676
186 5U1F 1 A, C, D BG505 DS-SOSIP gp120 UNP residues 29-502 11676
187 5THR 2 D, E, F BG505 SOSIP gp120 UNP residue 30-505 11676
188 5FUU 1 A, C, E HIV-1 ENVELOPE GLYCOPROTEIN GP160 GP120 OF JR-FL ENV GP120, RESIDUES 30-502 11676
189 3JCB 1 A, E, I Envelope glycoprotein gp120 SEE REMARK 999 11723
190 3JCC 1 A, E, I Envelope glycoprotein gp120 SEE REMARK 999 11723
191 5ACO 1 A, C, D HIV-1 ENVELOPE GLYCOPROTEIN THE ENV SEQUENCE IS FROM THE CLADE A VIRUS BG505, TRUNCATED AT RESIDUE 664 OF GP41, MUTATED TO HAVE THE N332 GLYCOSYLATION SITE, AND CONTAINS STABILIZING SOSIP MUTATIONS. GP120, RESIDUES 30-505 11676
192 5A8H 1 A, G, M HIV-1 GP120 11676
193 5A7X 1 A, E, I HIV-1 YU2 GP120 11676
194 3J70 4 D, P, U Envelope glycoprotein gp120 UNP residues 31-500 11676
195 3J5M 1 A, E, I BG505 SOSIP gp120 UNP residues 30-504 11676