5J4D

E. coli release factor 1 bound to the 70S ribosome in response to a pseudouridylated stop codon


Structural Similarities for the Entities in PDB 5J4D

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

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

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

Entity #1 | Chains A,FB

Description: 16S ribosomal RNA rna | Length: 1507

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


Entity #10 | Chains J,OB

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

No structure alignment results are available for 5J4D.J, 5J4D.OB explicitly.

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

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Entity #11 | Chains K,PB

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

No structure alignment results are available for 5J4D.K, 5J4D.PB explicitly.

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

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Entity #12 | Chains L,QB

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

No structure alignment results are available for 5J4D.L, 5J4D.QB explicitly.

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

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Entity #13 | Chains M,RB

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

No structure alignment results are available for 5J4D.M, 5J4D.RB explicitly.

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

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Entity #14 | Chains N,SB

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

No structure alignment results are available for 5J4D.N, 5J4D.SB explicitly.

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

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Entity #15 | Chains O,TB

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

No structure alignment results are available for 5J4D.O, 5J4D.TB explicitly.

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

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Entity #16 | Chains P,UB

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

No structure alignment results are available for 5J4D.P, 5J4D.UB explicitly.

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

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Entity #17 | Chains Q,VB

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

No structure alignment results are available for 5J4D.Q, 5J4D.VB explicitly.

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

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Entity #18 | Chains R,WB

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

No structure alignment results are available for 5J4D.R, 5J4D.WB explicitly.

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

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Entity #19 | Chains S,XB

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

No structure alignment results are available for 5J4D.S, 5J4D.XB explicitly.

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

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Entity #2 | Chains B,GB

Description: 25S ribosomal RNA rna | Length: 2880

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


Entity #20 | Chains T,YB

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

No structure alignment results are available for 5J4D.T, 5J4D.YB explicitly.

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

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Entity #21 | Chains U,ZB

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

No structure alignment results are available for 5J4D.U, 5J4D.ZB explicitly.

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

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Entity #22 | Chains AC,V

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

No structure alignment results are available for 5J4D.AC, 5J4D.V explicitly.

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

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Entity #23 | Chains BC,W

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

No structure alignment results are available for 5J4D.BC, 5J4D.W explicitly.

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

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Entity #24 | Chains CC,X

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

No structure alignment results are available for 5J4D.CC, 5J4D.X explicitly.

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

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Entity #25 | Chains DC,Y

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

No structure alignment results are available for 5J4D.DC, 5J4D.Y explicitly.

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

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Entity #26 | Chains EC,Z

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

No structure alignment results are available for 5J4D.EC, 5J4D.Z explicitly.

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

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Entity #27 | Chains AA,FC

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

No structure alignment results are available for 5J4D.AA, 5J4D.FC explicitly.

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

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Entity #28 | Chains BA,GC

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

No structure alignment results are available for 5J4D.BA, 5J4D.GC explicitly.

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

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Entity #29 | Chains CA,HC

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

No structure alignment results are available for 5J4D.CA, 5J4D.HC explicitly.

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

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Entity #3 | Chains C,HB

Description: 5S ribosomal RNA rna | Length: 120

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


Entity #30 | Chains DA,IC

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

No structure alignment results are available for 5J4D.DA, 5J4D.IC explicitly.

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

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Entity #31 | Chains EA,JC

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

No structure alignment results are available for 5J4D.EA, 5J4D.JC explicitly.

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

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Entity #32 | Chains FA,KC

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

No structure alignment results are available for 5J4D.FA, 5J4D.KC explicitly.

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

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Entity #33 | Chains GA,LC

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

No structure alignment results are available for 5J4D.GA, 5J4D.LC explicitly.

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

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Entity #34 | Chains HA,MC

Description: mRNA rna | Length: 27

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


Entity #35 | Chains JA,OC

Description: Peptide chain release factor 1 protein | Length: 368

No structure alignment results are available for 5J4D.JA, 5J4D.OC explicitly.

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

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Entity #36 | Chains KA,PC

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

No structure alignment results are available for 5J4D.KA, 5J4D.PC explicitly.

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

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Entity #37 | Chains LA,QC

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

No structure alignment results are available for 5J4D.LA, 5J4D.QC explicitly.

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

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Entity #38 | Chains MA,RC

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

No structure alignment results are available for 5J4D.MA, 5J4D.RC explicitly.

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

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Entity #39 | Chains NA,SC

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

No structure alignment results are available for 5J4D.NA, 5J4D.SC explicitly.

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

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Entity #4 | Chains D,IA,IB,NC

Description: tRNA rna | Length: 77

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


Entity #40 | Chains OA,TC

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

No structure alignment results are available for 5J4D.OA, 5J4D.TC explicitly.

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

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Entity #41 | Chains PA,UC

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

No structure alignment results are available for 5J4D.PA, 5J4D.UC explicitly.

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

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Entity #42 | Chains QA,VC

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

No structure alignment results are available for 5J4D.QA, 5J4D.VC explicitly.

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

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Entity #43 | Chains RA,WC

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

No structure alignment results are available for 5J4D.RA, 5J4D.WC explicitly.

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

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Entity #44 | Chains SA,XC

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

No structure alignment results are available for 5J4D.SA, 5J4D.XC explicitly.

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

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Entity #45 | Chains TA,YC

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

No structure alignment results are available for 5J4D.TA, 5J4D.YC explicitly.

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

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Entity #46 | Chains UA,ZC

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

No structure alignment results are available for 5J4D.UA, 5J4D.ZC explicitly.

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

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Entity #47 | Chains AD,VA

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

No structure alignment results are available for 5J4D.AD, 5J4D.VA explicitly.

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

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Entity #48 | Chains BD,WA

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

No structure alignment results are available for 5J4D.BD, 5J4D.WA explicitly.

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

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Entity #49 | Chains CD,XA

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

No structure alignment results are available for 5J4D.CD, 5J4D.XA explicitly.

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

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Entity #5 | Chains E,JB

Description: 50S ribosomal protein L2 protein | Length: 275

No structure alignment results are available for 5J4D.E, 5J4D.JB explicitly.

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

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Entity #50 | Chains DD,YA

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

No structure alignment results are available for 5J4D.DD, 5J4D.YA explicitly.

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

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Entity #51 | Chains ED,ZA

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

No structure alignment results are available for 5J4D.ED, 5J4D.ZA explicitly.

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

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Entity #52 | Chains AB,FD

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

No structure alignment results are available for 5J4D.AB, 5J4D.FD explicitly.

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

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Entity #53 | Chains BB,GD

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

No structure alignment results are available for 5J4D.BB, 5J4D.GD explicitly.

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

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Entity #54 | Chains CB,HD

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

No structure alignment results are available for 5J4D.CB, 5J4D.HD explicitly.

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

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Entity #55 | Chains DB,ID

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

No structure alignment results are available for 5J4D.DB, 5J4D.ID explicitly.

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

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Entity #6 | Chains F,KB

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

No structure alignment results are available for 5J4D.F, 5J4D.KB explicitly.

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

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Entity #7 | Chains G,LB

Description: 50S ribosomal protein L4 protein | Length: 205

No structure alignment results are available for 5J4D.G, 5J4D.LB explicitly.

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

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Entity #8 | Chains H,MB

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

No structure alignment results are available for 5J4D.H, 5J4D.MB explicitly.

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

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Entity #9 | Chains I,NB

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

No structure alignment results are available for 5J4D.I, 5J4D.NB explicitly.

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

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References