4Y4O

Crystal structure of the Thermus thermophilus 70S ribosome with rRNA modifications and bound to protein Y (YfiA) at 2.3A resolution


Structural Similarities for the Entities in PDB 4Y4O

The following structural similarities have been found using the jFATCAT-rigid algorithm [1,2].

To reduce the number of hits, a 40% sequence identity clustering has been applied and a representative chain taken from each cluster. If the representative chain consists of multiple domains, each domain is included in the search. If available, the SCOP 1.75 domain assignment [3] is used. Otherwise algorithmic domain assignments are computed using the ProteinDomainParser [4].

Currently viewing only significant results (P-value < 0.001). Show all available results.

Cluster data are up-to-date as of: Sep-27-2017

Info & Help Documentation



A detailed description of the procedure for the all vs. all alignments is available.

Entity #1 | Chains 1A,2A

Description: 23S Ribosomal RNA rna | Length: 2915

This entity is NOT a polypeptide entity and therefore cannot be considered for the all vs. all structure alignments.


Entity #10 | Chains 1O,2O

Description: 50S ribosomal protein L14 protein | Length: 122

No structure alignment results are available for 4Y4O.1O, 4Y4O.2O explicitly.

These chains are represented by chain 1WHI.a which has more than 70% sequence identity.

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Entity #11 | Chains 1P,2P

Description: 50S ribosomal protein L15 protein | Length: 150

No structure alignment results are available for 4Y4O.1P, 4Y4O.2P explicitly.

These chains are represented by chain XXXX.null which has more than 50% sequence identity.

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Entity #12 | Chains 1Q,2Q

Description: 50S ribosomal protein L16 protein | Length: 141

No structure alignment results are available for 4Y4O.1Q, 4Y4O.2Q explicitly.

These chains are represented by chain XXXX.null which has more than 50% sequence identity.

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Entity #13 | Chains 1R,2R

Description: 50S ribosomal protein L17 protein | Length: 118

No structure alignment results are available for 4Y4O.1R, 4Y4O.2R explicitly.

These chains are represented by chain XXXX.null which has more than 50% sequence identity.

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Entity #14 | Chains 1S,2S

Description: 50S ribosomal protein L18 protein | Length: 112

No structure alignment results are available for 4Y4O.1S, 4Y4O.2S explicitly.

These chains are represented by chain XXXX.null which has more than 50% sequence identity.

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Entity #15 | Chains 1T,2T

Description: 50S ribosomal protein L19 protein | Length: 146

No structure alignment results are available for 4Y4O.1T, 4Y4O.2T explicitly.

These chains are represented by chain XXXX.null which has more than 50% sequence identity.

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Entity #16 | Chains 1U,2U

Description: 50S ribosomal protein L20 protein | Length: 118

No structure alignment results are available for 4Y4O.1U, 4Y4O.2U explicitly.

These chains are represented by chain XXXX.null which has more than 50% sequence identity.

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Entity #17 | Chains 1V,2V

Description: 50S ribosomal protein L21 protein | Length: 101

No structure alignment results are available for 4Y4O.1V, 4Y4O.2V explicitly.

These chains are represented by chain XXXX.null which has more than 40% sequence identity.

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Entity #18 | Chains 1W,2W

Description: 50S ribosomal protein L22 protein | Length: 113

No structure alignment results are available for 4Y4O.1W, 4Y4O.2W explicitly.

These chains are represented by chain 1I4J.a which has more than 95% sequence identity.

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Entity #19 | Chains 1X,2X

Description: 50S ribosomal protein L23 protein | Length: 96

No structure alignment results are available for 4Y4O.1X, 4Y4O.2X explicitly.

These chains are represented by chain XXXX.null which has more than 40% sequence identity.

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Entity #2 | Chains 1B,2B

Description: 5S Ribosomal RNA rna | Length: 121

This entity is NOT a polypeptide entity and therefore cannot be considered for the all vs. all structure alignments.


Entity #20 | Chains 1Y,2Y

Description: 50S ribosomal protein L24 protein | Length: 110

No structure alignment results are available for 4Y4O.1Y, 4Y4O.2Y explicitly.

These chains are represented by chain XXXX.null which has more than 50% sequence identity.

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Entity #21 | Chains 1Z,2Z

Description: 50S ribosomal protein L25 protein | Length: 206

No structure alignment results are available for 4Y4O.1Z, 4Y4O.2Z explicitly.

These chains are represented by chain 1FEU.a which has more than 95% sequence identity.

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Entity #22 | Chains 10,20

Description: 50S ribosomal protein L27 protein | Length: 85

No structure alignment results are available for 4Y4O.10, 4Y4O.20 explicitly.

These chains are represented by chain XXXX.null which has more than 50% sequence identity.

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Entity #23 | Chains 11,21

Description: 50S ribosomal protein L28 protein | Length: 98

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Entity #24 | Chains 12,22

Description: 50S ribosomal protein L29 protein | Length: 72

No structure alignment results are available for 4Y4O.12, 4Y4O.22 explicitly.

These chains are represented by chain XXXX.null which has more than 95% sequence identity.

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Entity #25 | Chains 13,23

Description: 50S ribosomal protein L30 protein | Length: 60

No structure alignment results are available for 4Y4O.13, 4Y4O.23 explicitly.

These chains are represented by chain 1BXY.a which is 100% sequence identical.

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Entity #26 | Chains 14,24

Description: 50S ribosomal protein L31 protein | Length: 71

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Entity #27 | Chains 15,25

Description: 50S ribosomal protein L32 protein | Length: 60

No structure alignment results are available for 4Y4O.15, 4Y4O.25 explicitly.

These chains are represented by chain XXXX.null which has more than 40% sequence identity.

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Entity #28 | Chains 16,26

Description: 50S ribosomal protein L33 protein | Length: 54

No structure alignment results are available for 4Y4O.16, 4Y4O.26 explicitly.

These chains are represented by chain XXXX.null which has more than 40% sequence identity.

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Entity #29 | Chains 17,27

Description: 50S ribosomal protein L34 protein | Length: 49

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Entity #3 | Chains 1D,2D

Description: 50S ribosomal protein L2 protein | Length: 276

No structure alignment results are available for 4Y4O.1D, 4Y4O.2D explicitly.

These chains are represented by chain XXXX.null which has more than 50% sequence identity.

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Entity #30 | Chains 18,28

Description: 50S ribosomal protein L35 protein | Length: 65

No structure alignment results are available for 4Y4O.18, 4Y4O.28 explicitly.

These chains are represented by chain XXXX.null which has more than 40% sequence identity.

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Entity #31 | Chains 19,29

Description: 50S ribosomal protein L36 protein | Length: 37

No structure alignment results are available for 4Y4O.19, 4Y4O.29 explicitly.

These chains are represented by chain XXXX.null which has more than 50% sequence identity.

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Entity #32 | Chains 1a,2a

Description: 16S Ribosomal RNA rna | Length: 1521

This entity is NOT a polypeptide entity and therefore cannot be considered for the all vs. all structure alignments.


Entity #33 | Chains 1b,2b

Description: 30S ribosomal protein S2 protein | Length: 256

No structure alignment results are available for 4Y4O.1b, 4Y4O.2b explicitly.

These chains are represented by chain XXXX.null which has more than 50% sequence identity.

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Entity #34 | Chains 1c,2c

Description: 30S ribosomal protein S3 protein | Length: 239

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Entity #35 | Chains 1d,2d

Description: 30S ribosomal protein S4 protein | Length: 209

No structure alignment results are available for 4Y4O.1d, 4Y4O.2d explicitly.

These chains are represented by chain XXXX.null which has more than 50% sequence identity.

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Entity #36 | Chains 1e,2e

Description: 30S ribosomal protein S5 protein | Length: 162

No structure alignment results are available for 4Y4O.1e, 4Y4O.2e explicitly.

These chains are represented by chain XXXX.null which has more than 50% sequence identity.

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Entity #37 | Chains 1f,2f

Description: 30S ribosomal protein S6 protein | Length: 101

No structure alignment results are available for 4Y4O.1f, 4Y4O.2f explicitly.

These chains are represented by chain 1CQM.a which has more than 95% sequence identity.

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Entity #38 | Chains 1g,2g

Description: 30S ribosomal protein S7 protein | Length: 156

No structure alignment results are available for 4Y4O.1g, 4Y4O.2g explicitly.

These chains are represented by chain 1RSS.a which is 100% sequence identical.

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Entity #39 | Chains 1h,2h

Description: 30S ribosomal protein S8 protein | Length: 138

No structure alignment results are available for 4Y4O.1h, 4Y4O.2h explicitly.

These chains are represented by chain 1SEI.a which has more than 50% sequence identity.

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Entity #4 | Chains 1E,2E

Description: 50S ribosomal protein L3 protein | Length: 206

No structure alignment results are available for 4Y4O.1E, 4Y4O.2E explicitly.

These chains are represented by chain XXXX.null which has more than 50% sequence identity.

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Entity #40 | Chains 1i,2i

Description: 30S ribosomal protein S9 protein | Length: 128

No structure alignment results are available for 4Y4O.1i, 4Y4O.2i explicitly.

These chains are represented by chain XXXX.null which has more than 50% sequence identity.

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Entity #41 | Chains 1j,2j

Description: 30S ribosomal protein S10 protein | Length: 105

No structure alignment results are available for 4Y4O.1j, 4Y4O.2j explicitly.

These chains are represented by chain 3D3B.J which has more than 50% sequence identity.

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Entity #42 | Chains 1k,2k

Description: 30S ribosomal protein S11 protein | Length: 129

No structure alignment results are available for 4Y4O.1k, 4Y4O.2k explicitly.

These chains are represented by chain 4CVN.E which has more than 40% sequence identity.

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Entity #43 | Chains 1l,2l

Description: 30S ribosomal protein S12 protein | Length: 132

No structure alignment results are available for 4Y4O.1l, 4Y4O.2l explicitly.

These chains are represented by chain XXXX.null which has more than 70% sequence identity.

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Entity #44 | Chains 1m,2m

Description: 30S ribosomal protein S13 protein | Length: 126

No structure alignment results are available for 4Y4O.1m, 4Y4O.2m explicitly.

These chains are represented by chain XXXX.null which has more than 50% sequence identity.

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Entity #45 | Chains 1n,2n

Description: 30S ribosomal protein S14 type Z protein | Length: 61

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Entity #46 | Chains 1o,2o

Description: 30S ribosomal protein S15 protein | Length: 89

No structure alignment results are available for 4Y4O.1o, 4Y4O.2o explicitly.

These chains are represented by chain 4A5U.B which has more than 50% sequence identity.

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Entity #47 | Chains 1p,2p

Description: 30S ribosomal protein S16 protein | Length: 88

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Entity #48 | Chains 1q,2q

Description: 30S ribosomal protein S17 protein | Length: 105

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Entity #49 | Chains 1r,2r

Description: 30S ribosomal protein S18 protein | Length: 88

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Entity #5 | Chains 1F,2F

Description: 50S ribosomal protein L4 protein | Length: 210

No structure alignment results are available for 4Y4O.1F, 4Y4O.2F explicitly.

These chains are represented by chain 1DMG.a which has more than 40% sequence identity.

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Entity #50 | Chains 1s,2s

Description: 30S ribosomal protein S19 protein | Length: 93

No structure alignment results are available for 4Y4O.1s, 4Y4O.2s explicitly.

These chains are represented by chain XXXX.null which is 100% sequence identical.

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Entity #51 | Chains 1t,2t

Description: 30S ribosomal protein S20 protein | Length: 106

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Entity #52 | Chains 1u,2u

Description: 30S ribosomal protein Thx protein | Length: 27

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Entity #53 | Chains 1y,2y

Description: Ribosome-associated inhibitor A protein | Length: 113

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Entity #6 | Chains 1G,2G

Description: 50S ribosomal protein L5 protein | Length: 182

No structure alignment results are available for 4Y4O.1G, 4Y4O.2G explicitly.

These chains are represented by chain 1IQ4.a which has more than 50% sequence identity.

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Entity #7 | Chains 1H,2H

Description: 50S ribosomal protein L6 protein | Length: 180

No structure alignment results are available for 4Y4O.1H, 4Y4O.2H explicitly.

These chains are represented by chain XXXX.null which has more than 40% sequence identity.

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Entity #8 | Chains 1I,2I

Description: 50S ribosomal protein L9 protein | Length: 148

No structure alignment results are available for 4Y4O.1I, 4Y4O.2I explicitly.

These chains are represented by chain XXXX.null which has more than 40% sequence identity.

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Entity #9 | Chains 1N,2N

Description: 50S ribosomal protein L13 protein | Length: 140

No structure alignment results are available for 4Y4O.1N, 4Y4O.2N explicitly.

These chains are represented by chain XXXX.null which has more than 50% sequence identity.

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References