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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 # 1007 Members. Sequence cutoff: 70% Cluster size: 34 sequences
Rank   PDB id Entity id Chains Description Details Taxonomy EC Number
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1 4H8W 4 C T-cell surface glycoprotein CD4 9606  
2 2NXY 2 B T-cell surface glycoprotein CD4 D1D2, N-TERMINAL TWO DOMAIN FRAGMENT 9606  
3 2NY2 2 B T-cell surface glycoprotein CD4 D1D2, N-TERMINAL TWO DOMAIN FRAGMENT 9606  
4 1CDY 1 A T-CELL SURFACE GLYCOPROTEIN CD4 D1D2 FRAGMENT 9606  
5 2NY4 2 B T-cell surface glycoprotein CD4 D1D2, N-TERMINAL TWO DOMAIN FRAGMENT 9606  
6 2NY3 2 B T-cell surface glycoprotein CD4 D1D2, N-TERMINAL TWO DOMAIN FRAGMENT 9606  
7 2NY1 2 B T-cell surface glycoprotein CD4 D1D2, N-TERMINAL TWO DOMAIN FRAGMENT 9606  
8 2NXZ 2 B T-cell surface glycoprotein CD4 D1D2, N-TERMINAL TWO DOMAIN FRAGMENT 9606  
9 3O2D 3 A T-cell surface glycoprotein CD4 UNP residues 26-207 9606  
10 3CD4 1 A T CELL SURFACE GLYCOPROTEIN CD4 9606  
11 2NY0 2 B T-cell surface glycoprotein CD4 D1D2, N-TERMINAL TWO DOMAIN FRAGMENT 9606  
12 3S5L 4 G, H T-cell surface glycoprotein CD4 CD4 9606  
13 1CDH 1 A T CELL SURFACE GLYCOPROTEIN CD4 9606  
14 1CDU 1 A T-CELL SURFACE GLYCOPROTEIN CD4 D1D2 FRAGMENT 9606  
15 1CDJ 1 A T-CELL SURFACE GLYCOPROTEIN CD4 WILD TYPE, 110K FORM D1D2 FRAGMENT 9606  
16 2NY5 2 C T-cell surface glycoprotein CD4 D1D2, N-TERMINAL TWO DOMAIN FRAGMENT 9606  
17 1RZJ 2 C T-CELL SURFACE GLYCOPROTEIN CD4 D1D2, N-TERMINAL TWO DOMAIN FRAGMENT 9606  
18 1GC1 2 C CD4 D1D2, N-TERMINAL TWO DOMAIN FRAGMENT 9606  
19 1G9M 2 C T-CELL SURFACE GLYCOPROTEIN CD4 D1D2, N-TERMINAL TWO DOMAIN FRAGMENT 9606  
20 3JWD 2 C, D T-cell surface glycoprotein CD4 9606  
21 3S4S 4 G, H T-cell surface glycoprotein CD4 UNP residues 26-203 9606  
22 1CDI 1 A T CELL SURFACE GLYCOPROTEIN CD4 9606  
23 2NY6 2 B T-cell surface glycoprotein CD4 D1D2, N-TERMINAL TWO DOMAIN FRAGMENT 9606  
24 1RZK 2 C T-CELL SURFACE GLYCOPROTEIN CD4 D1D2, N-TERMINAL TWO DOMAIN FRAGMENT 9606  
25 1G9N 2 C T-CELL SURFACE GLYCOPROTEIN CD4 D1D2, N-TERMINAL TWO DOMAIN FRAGMENT 9606  
26 2QAD 2 B, F T-cell surface glycoprotein CD4 D1D2, IG-LIKE V-TYPE AND IG-LIKE C2-TYPE 1 DOMAINS 9606  
27 4P9H 1 C T-cell surface glycoprotein CD4 CD4 D1D2 9606  
28 4R2G 2 B, F, H, L T-cell surface glycoprotein CD4 9606  
29 4JM2 6 F T-cell surface glycoprotein CD4 Ig-like V-type and C2-type 1 domains (UNP residues 26-208) 9606  
30 3LQA 1 C T-cell surface glycoprotein CD4 9606  
31 3JWO 2 C T-cell surface glycoprotein CD4 9606  
32 2B4C 2 C T-cell surface glycoprotein CD4 D1D2, N-TERMINAL TWO DOMAIN FRAGMENT 9606  
33 4R4H 2 B T-cell surface glycoprotein CD4 UNP residues 26-203 9606  
34 1JL4 4 D T-CELL SURFACE GLYCOPROTEIN CD4 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 25754
95% 1 2 16728
90% 1 2 16304
70% 37 57 349
50% 37 57 385
40% 37 57 406
30% 37 57 415
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 29 857
95% 20 34 960
90% 20 34 978
70% 20 34 1007
50% 20 34 1057
40% 20 34 1086
30% 20 34 1063
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 11459
95% 41 107 74
90% 203 374 5
70% 749 1320 3
50% 1787 3142 1
40% 1788 3143 1
30% 2026 3719 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 11418
95% 2 4 10983
90% 2 4 10818
70% 867 1514 2
50% 1788 3142 1
40% 1789 3143 1
30% 2027 3719 1
 

Documentation

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