Structural Similarities for the Entities in PDB 5GMK

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.

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Entity #1 | Chains A

Description: Pre-mRNA-splicing factor 8 protein | Length: 2413

No structure alignment results are available for 5GMK.A explicitly.

It is represented by chain XXXX.null which is 100% sequence identical.

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Entity #10 | Chains O

Description: Pre-mRNA-splicing factor PRP46 protein | Length: 451

No structure alignment results are available for 5GMK.O explicitly.

It is represented by chain XXXX.null which has more than 95% sequence identity.

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Entity #11 | Chains P

Description: Pre-mRNA-processing protein 45 protein | Length: 379

No structure alignment results are available for 5GMK.P explicitly.

It is represented by chain XXXX.null which is 100% sequence identical.

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Entity #12 | Chains Q

Description: Pre-mRNA-splicing factor SLT11 protein | Length: 364

No structure alignment results are available for 5GMK.Q explicitly.

It is represented by chain XXXX.null which is 100% sequence identical.

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Entity #13 | Chains R

Description: Pre-mRNA-splicing factor CWC2 protein | Length: 339

No structure alignment results are available for 5GMK.R explicitly.

It is represented by chain XXXX.null which is 100% sequence identical.

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Entity #14 | Chains S

Description: Pre-mRNA-splicing factor CWC15 protein | Length: 175

No structure alignment results are available for 5GMK.S explicitly.

It is represented by chain XXXX.null which has more than 95% sequence identity.

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Entity #15 | Chains T

Description: Pre-mRNA-splicing factor BUD31 protein | Length: 157

No structure alignment results are available for 5GMK.T explicitly.

It is represented by chain XXXX.null which is 100% sequence identical.

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Entity #16 | Chains Z

Description: Pre-mRNA-splicing factor CWC22 protein | Length: 577

No structure alignment results are available for 5GMK.Z explicitly.

It is represented by chain XXXX.null which is 100% sequence identical.

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Entity #17 | Chains c

Description: Pre-mRNA-splicing factor CEF1 protein | Length: 587

No structure alignment results are available for 5GMK.c explicitly.

It is represented by chain 5WSG.c which is 100% sequence identical.

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Entity #18 | Chains d

Description: Pre-mRNA-splicing factor CLF1 protein | Length: 687

No structure alignment results are available for 5GMK.d explicitly.

It is represented by chain 5WSG.d which is 100% sequence identical.

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Entity #19 | Chains F

Description: Protein CWC16 protein | Length: 278

No structure alignment results are available for 5GMK.F explicitly.

It is represented by chain XXXX.null which is 100% sequence identical.

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Entity #2 | Chains C

Description: Pre-mRNA-splicing factor SNU114 protein | Length: 1008

No structure alignment results are available for 5GMK.C explicitly.

It is represented by chain XXXX.null which is 100% sequence identical.

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Entity #20 | Chains G

Description: Pre-mRNA-splicing factor CWC25 protein | Length: 179

No structure alignment results are available for 5GMK.G explicitly.

It is represented by chain 5LJ3.F which is 100% sequence identical.

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Entity #21 | Chains H

Description: Pre-mRNA-splicing factor ISY1 protein | Length: 235

No structure alignment results are available for 5GMK.H explicitly.

It is represented by chain 5LJ3.G which has more than 95% sequence identity.

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Entity #22 | Chains I

Description: Pre-mRNA-splicing factor SYF2 protein | Length: 215

No structure alignment results are available for 5GMK.I explicitly.

It is represented by chain XXXX.null which is 100% sequence identical.

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Entity #23 | Chains v

Description: Pre-mRNA-splicing factor SYF1 protein | Length: 859

No structure alignment results are available for 5GMK.v explicitly.

It is represented by chain 5WSG.v which is 100% sequence identical.

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Entity #24 | Chains n

Description: Pre-mRNA-processing factor 17 protein | Length: 455

No structure alignment results are available for 5GMK.n explicitly.

It is represented by chain XXXX.null which is 100% sequence identical.

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Entity #25 | Chains o,p,q,r

Description: Pre-mRNA-processing factor 19 protein | Length: 503

No structure alignment results are available for 5GMK.o, 5GMK.p, 5GMK.q, 5GMK.r explicitly.

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

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Entity #26 | Chains t

Description: Pre-mRNA-splicing factor SNT309 protein | Length: 175

No structure alignment results are available for 5GMK.t explicitly.

It is represented by chain XXXX.null which is 100% sequence identical.

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Entity #27 | Chains k,s

Description: Small nuclear ribonucleoprotein-associated protein B protein | Length: 196

No structure alignment results are available for 5GMK.k, 5GMK.s explicitly.

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

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Entity #28 | Chains i,u

Description: Small nuclear ribonucleoprotein E protein | Length: 94

No structure alignment results are available for 5GMK.i, 5GMK.u explicitly.

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

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Entity #29 | Chains h,w

Description: Small nuclear ribonucleoprotein F protein | Length: 86

No structure alignment results are available for 5GMK.h, 5GMK.w explicitly.

These chains are represented by chain 1N9R.a which is 100% sequence identical.

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Entity #3 | Chains D

Description: U5 snRNA rna | Length: 214

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


Entity #30 | Chains j,x

Description: Small nuclear ribonucleoprotein G protein | Length: 77

No structure alignment results are available for 5GMK.j, 5GMK.x explicitly.

These chains are represented by chain 4F7U.G which has more than 30% sequence identity.

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Entity #31 | Chains l,y

Description: Small nuclear ribonucleoprotein Sm D3 protein | Length: 101

No structure alignment results are available for 5GMK.l, 5GMK.y explicitly.

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

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Entity #32 | Chains m,z

Description: Small nuclear ribonucleoprotein Sm D1 protein | Length: 146

No structure alignment results are available for 5GMK.m, 5GMK.z explicitly.

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

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Entity #33 | Chains e,g

Description: Small nuclear ribonucleoprotein Sm D2 protein | Length: 110

No structure alignment results are available for 5GMK.e, 5GMK.g explicitly.

These chains are represented by chain 4F7U.B which has more than 50% sequence identity.

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Entity #34 | Chains a

Description: U2 small nuclear ribonucleoprotein B'' protein | Length: 111

No structure alignment results are available for 5GMK.a explicitly.

It is represented by chain XXXX.null which is 100% sequence identical.

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Entity #35 | Chains b

Description: U2 small nuclear ribonucleoprotein A' protein | Length: 238

No structure alignment results are available for 5GMK.b explicitly.

It is represented by chain XXXX.null which is 100% sequence identical.

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Entity #4 | Chains E

Description: U6 snRNA rna | Length: 112

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


Entity #5 | Chains L

Description: U2 snRNA rna | Length: 1175

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


Entity #6 | Chains M

Description: Intron_BPS rna | Length: 29

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


Entity #7 | Chains B

Description: 5'-Exon rna | Length: 13

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


Entity #8 | Chains N

Description: 5'-Splicing Site rna | Length: 15

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


Entity #9 | Chains J

Description: Pre-mRNA-splicing factor CWC21 protein | Length: 135

No structure alignment results are available for 5GMK.J explicitly.

It is represented by chain XXXX.null which is 100% sequence identical.

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References