3CC2

The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with rrnA Sequence for the 23S rRNA and Genome-derived Sequences for r-Proteins


Sequence Similarity Clusters for the Entities in PDB 3CC2

Entity #1 | Chains: A
50S ribosomal protein L2P protein, length: 240 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 8 47 838
95 % 9 68 728 Flexibility: No
Max RMSD: 0.6, Avg RMSD: 0.3
PDBFlex
90 % 9 68 756
70 % 9 68 805
50 % 9 187 206
40 % 11 560 22
30 % 11 560 39
Entity #10 | Chains: J
50S ribosomal protein L13P protein, length: 145 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 9 74 472
95 % 9 74 650
90 % 9 74 676
70 % 9 74 726
50 % 9 74 781
40 % 10 77 780
30 % 10 78 768
Entity #11 | Chains: K
50S ribosomal protein L14P protein, length: 132 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 3 44 916
95 % 9 68 735
90 % 9 68 764
70 % 9 68 817
50 % 9 197 201
40 % 12 583 20
30 % 12 583 35
Entity #12 | Chains: L
50S ribosomal protein L15P protein, length: 165 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 9 74 470
95 % 9 74 649 Flexibility: No
Max RMSD: 1.9, Avg RMSD: 0.3
PDBFlex
90 % 9 74 675
70 % 9 74 725
50 % 9 74 778
40 % 9 74 817
30 % 11 558 40
Entity #13 | Chains: M
50S ribosomal protein L15e protein, length: 196 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 2 23 2187
95 % 8 47 1157 Flexibility: No
Max RMSD: 0.6, Avg RMSD: 0.2
PDBFlex
90 % 8 47 1180
70 % 9 68 808
50 % 9 196 203
40 % 9 196 216
30 % 9 196 227
Entity #14 | Chains: N
50S ribosomal protein L18P protein, length: 187 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 9 74 468
95 % 9 74 647
90 % 9 74 673
70 % 9 74 721
50 % 9 76 755
40 % 9 76 792
30 % 9 79 748
Entity #15 | Chains: O
50S ribosomal protein L18e protein, length: 116 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 9 68 542
95 % 9 68 737 Flexibility: No
Max RMSD: 0.5, Avg RMSD: 0.2
PDBFlex
90 % 9 68 767
70 % 9 68 820
50 % 9 70 828
40 % 9 70 868
30 % 9 70 853
Entity #16 | Chains: P
50S ribosomal protein L19e protein, length: 149 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 8 47 845
95 % 9 68 734 Flexibility: No
Max RMSD: 0.5, Avg RMSD: 0.2
PDBFlex
90 % 9 68 763
70 % 9 68 816
50 % 9 68 859
40 % 9 72 838
30 % 9 72 831
Entity #17 | Chains: Q
50S ribosomal protein L21e protein, length: 96 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 9 68 544
95 % 9 68 739 Flexibility: No
Max RMSD: 0.4, Avg RMSD: 0.2
PDBFlex
90 % 9 68 769
70 % 9 68 822
50 % 9 70 829
40 % 9 70 869
30 % 9 71 843
Entity #18 | Chains: R
50S ribosomal protein L22P protein, length: 155 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 9 67 556
95 % 9 68 732
90 % 9 68 761
70 % 9 68 813
50 % 9 68 856
40 % 9 68 895
30 % 9 199 223
Entity #19 | Chains: S
50S ribosomal protein L23P protein, length: 85 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 9 74 475
95 % 9 74 653 Flexibility: No
Max RMSD: 1.3, Avg RMSD: 0.3
PDBFlex
90 % 9 74 680
70 % 9 74 728
50 % 9 77 749
40 % 9 79 753
30 % 11 449 65
Entity #2 | Chains: B
50S ribosomal protein L3P protein, length: 338 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 9 67 551
95 % 9 74 638 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.2
PDBFlex
90 % 9 74 667
70 % 9 74 716
50 % 9 74 771
40 % 9 202 210
30 % 9 202 219
Entity #20 | Chains: T
50S ribosomal protein L24P protein, length: 120 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 9 74 474
95 % 9 74 652 Flexibility: No
Max RMSD: 0.4, Avg RMSD: 0.2
PDBFlex
90 % 9 74 679
70 % 9 74 727
50 % 9 203 195
40 % 9 204 208
30 % 9 204 218
Entity #21 | Chains: U
50S ribosomal protein L24e protein, length: 67 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 9 70 510
95 % 9 70 703 Flexibility: No
Max RMSD: 0.8, Avg RMSD: 0.2
PDBFlex
90 % 9 70 730
70 % 9 70 779
50 % 9 70 831
40 % 9 70 871
30 % 9 70 856
Entity #22 | Chains: V
50S ribosomal protein L29P protein, length: 71 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 9 74 476
95 % 9 74 654 Flexibility: No
Max RMSD: 0.9, Avg RMSD: 0.3
PDBFlex
90 % 9 74 681
70 % 9 74 729
50 % 9 74 782
40 % 11 409 52
30 % 11 435 67
Entity #23 | Chains: W
50S ribosomal protein L30P protein, length: 154 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 9 68 540
95 % 9 68 733 Flexibility: No
Max RMSD: 0.4, Avg RMSD: 0.2
PDBFlex
90 % 9 68 762
70 % 9 68 814
50 % 9 68 857
40 % 9 70 867
30 % 9 71 840
Entity #24 | Chains: X
50S ribosomal protein L31e protein, length: 92 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 9 68 546
95 % 9 68 741 Flexibility: No
Max RMSD: 2.2, Avg RMSD: 0.3
PDBFlex
90 % 9 68 771
70 % 9 68 824
50 % 9 68 864
40 % 9 68 898
30 % 9 68 880
Entity #25 | Chains: Y
50S ribosomal protein L32e protein, length: 241 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 9 63 595
95 % 9 63 818 Flexibility: No
Max RMSD: 0.4, Avg RMSD: 0.2
PDBFlex
90 % 9 63 849
70 % 9 63 888
50 % 9 63 931
40 % 9 63 961
30 % 9 63 945
Entity #26 | Chains: Z
50S ribosomal protein L37Ae protein, length: 116 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 1 17 3191
95 % 1 17 3947 Flexibility: No
Max RMSD: 0.9, Avg RMSD: 0.5
PDBFlex
90 % 1 17 4003
70 % 1 17 3948
50 % 1 17 3840
40 % 1 17 3685
30 % 1 17 3449
Entity #27 | Chains: 1
50S ribosomal protein L37e protein, length: 57 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 9 68 547
95 % 9 68 742 Flexibility: No
Max RMSD: 0.4, Avg RMSD: 0.2
PDBFlex
90 % 9 68 772
70 % 9 68 825
50 % 9 69 843
40 % 9 69 883
30 % 9 69 867
Entity #28 | Chains: 2
50S ribosomal protein L39e protein, length: 50 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 8 47 850
95 % 9 68 743 Flexibility: No
Max RMSD: 0.6, Avg RMSD: 0.3
PDBFlex
90 % 9 68 773
70 % 9 68 826
50 % 9 189 204
40 % 9 189 222
30 % 9 189 233
Entity #29 | Chains: 3
50S ribosomal protein L44E protein, length: 92 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 9 68 545
95 % 9 68 740 Flexibility: No
Max RMSD: 1.2, Avg RMSD: 0.4
PDBFlex
90 % 9 68 770
70 % 9 68 823
50 % 9 68 863
40 % 9 68 897
30 % 9 184 237
Entity #3 | Chains: C
50S ribosomal protein L4P protein, length: 246 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 2 23 2181
95 % 9 74 641 Flexibility: No
Max RMSD: 0.7, Avg RMSD: 0.2
PDBFlex
90 % 9 74 670
70 % 9 74 718
50 % 9 74 773
40 % 9 76 788
30 % 10 78 762
Entity #30 | Chains: 0
23S RIBOSOMAL RNA rna, length: 2923 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #31 | Chains: 9
5S RIBOSOMAL RNA rna, length: 122 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #4 | Chains: D
50S ribosomal protein L5P protein, length: 177 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 9 74 469
95 % 9 74 648 Flexibility: No
Max RMSD: 1.1, Avg RMSD: 0.4
PDBFlex
90 % 9 74 674
70 % 9 74 722
50 % 9 74 775
40 % 10 196 215
30 % 10 196 225
Entity #5 | Chains: E
50S ribosomal protein L6P protein, length: 178 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 9 68 539
95 % 9 68 731 Flexibility: No
Max RMSD: 0.4, Avg RMSD: 0.2
PDBFlex
90 % 9 68 759
70 % 9 68 811
50 % 9 68 855
40 % 9 194 218
30 % 12 573 38
Entity #6 | Chains: F
50S ribosomal protein L7Ae protein, length: 120 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 8 47 846
95 % 8 47 1161 Flexibility: No
Max RMSD: 0.5, Avg RMSD: 0.3
PDBFlex
90 % 9 68 766
70 % 9 68 819
50 % 20 107 388
40 % 25 128 286
30 % 25 130 293
Entity #7 | Chains: G
50S ribosomal protein L10E protein, length: 348 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 1 20 2526
95 % 8 64 789 Flexibility: No
Max RMSD: 0.5, Avg RMSD: 0.3
PDBFlex
90 % 8 64 821
70 % 8 64 863
50 % 8 64 917
40 % 8 64 941
30 % 8 65 915
Entity #8 | Chains: H
50S ribosomal protein L10e protein, length: 177 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 8 47 843
95 % 8 47 1159 Flexibility: No
Max RMSD: 0.4, Avg RMSD: 0.2
PDBFlex
90 % 8 47 1184
70 % 8 47 1209
50 % 9 74 776
40 % 9 79 752
30 % 9 79 750
Entity #9 | Chains: I
50S ribosomal protein L11P protein, length: 162 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 8 42 967
95 % 8 42 1300 Flexibility: Low
Max RMSD: 1.2, Avg RMSD: 0.6
PDBFlex
90 % 8 42 1328
70 % 8 42 1354
50 % 9 46 1231
40 % 9 46 1241
30 % 9 89 620

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.

You can also use the structure comparison tool to compare any 2 given structures