Structural Similarities for the Entities in PDB 6O9L

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: DNA-directed RNA polymerase II subunit RPB1 protein | Length: 1970

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Entity #10 | Chains J

Description: DNA-directed RNA polymerases I, II, and III subunit RPABC5 protein | Length: 67

No structure alignment results are available for 6O9L.J explicitly.

It is represented by chain 4C2M.J which has more than 70% sequence identity.

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Entity #11 | Chains K

Description: DNA-directed RNA polymerase II subunit RPB11-a protein | Length: 117

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Entity #12 | Chains L

Description: DNA-directed RNA polymerases I, II, and III subunit RPABC4 protein | Length: 58

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Entity #13 | Chains M

Description: Transcription initiation factor IIB protein | Length: 316

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Entity #14 | Chains N

Description: Transcription initiation factor IIA subunit 1 protein | Length: 376

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Entity #15 | Chains O

Description: Transcription initiation factor IIA subunit 2 protein | Length: 109

No structure alignment results are available for 6O9L.O explicitly.

It is represented by chain 1NVP.d which is 100% sequence identical.

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Entity #16 | Chains P

Description: TATA-box-binding protein protein | Length: 339

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Entity #17 | Chains Q

Description: General transcription factor IIE subunit 1 protein | Length: 439

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Entity #18 | Chains R

Description: Transcription initiation factor IIE subunit beta protein | Length: 291

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Entity #19 | Chains S

Description: General transcription factor IIF subunit 1 protein | Length: 517

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Entity #2 | Chains B

Description: DNA-directed RNA polymerase II subunit RPB2 protein | Length: 1174

No structure alignment results are available for 6O9L.B explicitly.

It is represented by chain 1TWF.b which has more than 30% sequence identity.

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Entity #20 | Chains T

Description: General transcription factor IIF subunit 2 protein | Length: 249

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Entity #21 | Chains U

Description: Transcription elongation factor A protein 1 protein | Length: 301

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Entity #22 | Chains 0

Description: TFIIH basal transcription factor complex helicase XPD subunit protein | Length: 760

No structure alignment results are available for 6O9L.0 explicitly.

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

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Entity #23 | Chains 1

Description: General transcription factor IIH subunit 1 protein | Length: 548

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Entity #24 | Chains 2

Description: General transcription factor IIH subunit 4, p52 protein | Length: 462

No structure alignment results are available for 6O9L.2 explicitly.

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

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Entity #25 | Chains 3

Description: CDK-activating kinase assembly factor MAT1 protein | Length: 309

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Entity #26 | Chains 4

Description: General transcription factor IIH subunit 3 protein | Length: 308

No structure alignment results are available for 6O9L.4 explicitly.

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

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Entity #27 | Chains 5

Description: General transcription factor IIH subunit 5 protein | Length: 71

No structure alignment results are available for 6O9L.5 explicitly.

It is represented by chain 1YDL.a which has more than 70% sequence identity.

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Entity #28 | Chains 6

Description: General transcription factor IIH subunit 2 protein | Length: 395

No structure alignment results are available for 6O9L.6 explicitly.

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

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Entity #29 | Chains 7

Description: TFIIH basal transcription factor complex helicase XPB subunit protein | Length: 782

No structure alignment results are available for 6O9L.7 explicitly.

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

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Entity #3 | Chains C

Description: DNA-directed RNA polymerase II subunit RPB3 protein | Length: 275

No structure alignment results are available for 6O9L.C explicitly.

It is represented by chain 5IP7.C which has more than 40% sequence identity.

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Entity #30 | Chains 8

Description: Cyclin-dependent kinase 7 protein | Length: 346

No structure alignment results are available for 6O9L.8 explicitly.

It is represented by chain 1UA2.a which is 100% sequence identical.

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Entity #31 | Chains 9

Description: Cyclin-H protein | Length: 323

No structure alignment results are available for 6O9L.9 explicitly.

It is represented by chain 1KXU.a which is 100% sequence identical.

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Entity #32 | Chains X

Description: DNA (65-MER) dna | Length: 65

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


Entity #33 | Chains Y

Description: DNA (65-MER) dna | Length: 65

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


Entity #4 | Chains D

Description: DNA-directed RNA polymerase II subunit RPB4 protein | Length: 142

No structure alignment results are available for 6O9L.D explicitly.

It is represented by chain 2C35.a which is 100% sequence identical.

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Entity #5 | Chains E

Description: DNA-directed RNA polymerase II subunit RPB5 protein | Length: 210

No structure alignment results are available for 6O9L.E explicitly.

It is represented by chain 1DZF.a which has more than 40% sequence identity.

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Entity #6 | Chains F

Description: DNA-directed RNA polymerases I, II, and III subunit RPABC2 protein | Length: 127

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Entity #7 | Chains G

Description: DNA-directed RNA polymerase II subunit RPB7 protein | Length: 172

No structure alignment results are available for 6O9L.G explicitly.

It is represented by chain 1Y14.b which has more than 50% sequence identity.

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Entity #8 | Chains H

Description: DNA-directed RNA polymerases I, II, and III subunit RPABC3 protein | Length: 150

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Entity #9 | Chains I

Description: DNA-directed RNA polymerase II subunit RPB9 protein | Length: 125

No structure alignment results are available for 6O9L.I explicitly.

It is represented by chain 1TWF.i which has more than 30% sequence identity.

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References