POP-OUT | CLOSE
 
CRYSTAL STRUCTURE OF THE RIBOSOME AT 5.5 A RESOLUTION. THIS FILE, 1GIY, CONTAINS THE 50S RIBOSOME SUBUNIT. THE 30S RIBOSOME SUBUNIT, THREE TRNA, AND MRNA MOLECULES ARE IN THE FILE 1GIX
1GIY

Structural Similarities for the Entities in PDB 1GIY

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].

Entity #1: Chains: A
Description: 50S 23S RIBOSOMAL RNA rna
Length: 2916

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

 




Entity #10: Chains: K
Description: 50S RIBOSOMAL PROTEIN L9 protein
Length: 149
No structure alignment results are available for 1GIY.K explicitly.

It is represented by chain 1DIV.A which is 100% sequence identical.

 Click here to show the structure comparison results for representative 1DIV.A

 
 
  Loading...

To see how chain 1GIY.K compares with the representative chain d1diva1 select a method below:





Entity #11: Chains: L
Description: 50S RIBOSOMAL PROTEIN L11 protein
Length: 141
No structure alignment results are available for 1GIY.L explicitly.

It is represented by chain 3EGV.B which has more than 50% sequence identity.

 Click here to show the structure comparison results for representative 3EGV.B

 
 
  Loading...

To see how chain 1GIY.L compares with the representative chain d3egvb1 select a method below:





Entity #12: Chains: M
Description: 50S RIBOSOMAL PROTEIN L13 protein
Length: 145
No structure alignment results are available for 1GIY.M explicitly.

It is represented by chain 1J3A.A which has more than 40% sequence identity.

 Click here to show the structure comparison results for representative 1J3A.A

 
 
  Loading...

To see how chain 1GIY.M compares with the representative chain d1j3aa_ select a method below:





Entity #13: Chains: N
Description: 50S RIBOSOMAL PROTEIN L14 protein
Length: 122
No structure alignment results are available for 1GIY.N explicitly.

It is represented by chain 1WHI.A which is 100% sequence identical.

 Click here to show the structure comparison results for representative 1WHI.A

 
 
  Loading...

To see how chain 1GIY.N compares with the representative chain d1whia_ select a method below:





Entity #14: Chains: O
Description: 50S RIBOSOMAL PROTEIN L15 protein
Length: 164
No structure alignment results are available for 1GIY.O explicitly.

It is represented by chain 4HUB.L which is 100% sequence identical.

 Click here to show the structure comparison results for representative 4HUB.L

 
 
  Loading...

To see how chain 1GIY.O compares with the representative chain PDP:4HUBLa select a method below:





Entity #15: Chains: P
Description: 50S RIBOSOMAL PROTEIN L16 protein
Length: 138
No structure alignment results are available for 1GIY.P explicitly.

It is represented by chain 4HUB.H which has more than 50% sequence identity.

 Click here to show the structure comparison results for representative 4HUB.H

 
 
  Loading...

To see how chain 1GIY.P compares with the representative chain PDP:4HUBHa select a method below:





Entity #16: Chains: Q
Description: 50S RIBOSOMAL PROTEIN L18 protein
Length: 186
No structure alignment results are available for 1GIY.Q explicitly.

It is represented by chain 4HUB.N which is 100% sequence identical.

 Click here to show the structure comparison results for representative 4HUB.N

 
 
  Loading...

To see how chain 1GIY.Q compares with the representative chain PDP:4HUBNa select a method below:





Entity #17: Chains: R
Description: 50S RIBOSOMAL PROTEIN L19 protein
Length: 66
No structure alignment results are available for 1GIY.R explicitly.

It is represented by chain 4HUB.U which is 100% sequence identical.

 Click here to show the structure comparison results for representative 4HUB.U

 
 
  Loading...

To see how chain 1GIY.R compares with the representative chain PDP:4HUBUa select a method below:





Entity #18: Chains: S
Description: 50S RIBOSOMAL PROTEIN L22 protein
Length: 113
No structure alignment results are available for 1GIY.S explicitly.

It is represented by chain 1I4J.A which has more than 95% sequence identity.

 Click here to show the structure comparison results for representative 1I4J.A

 
 
  Loading...

To see how chain 1GIY.S compares with the representative chain d1i4ja_ select a method below:





Entity #19: Chains: T
Description: 50S RIBOSOMAL PROTEIN L23 protein
Length: 84
No structure alignment results are available for 1GIY.T explicitly.

It is represented by chain 4HUB.S which is 100% sequence identical.

 Click here to show the structure comparison results for representative 4HUB.S

 
 
  Loading...

To see how chain 1GIY.T compares with the representative chain PDP:4HUBSa select a method below:





Entity #2: Chains: B
Description: 50S 5S RIBOSOMAL RNA rna
Length: 123

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

 




Entity #20: Chains: U
Description: 50S RIBOSOMAL PROTEIN L24 protein
Length: 119
No structure alignment results are available for 1GIY.U explicitly.

It is represented by chain 4HUB.T which is 100% sequence identical.

 Click here to show the structure comparison results for representative 4HUB.T

 
 
  Loading...

To see how chain 1GIY.U compares with the representative chain PDP:4HUBTa select a method below:





Entity #21: Chains: V
Description: 50S RIBOSOMAL PROTEIN L25 protein
Length: 94
No structure alignment results are available for 1GIY.V explicitly.

It is represented by chain 1DFU.P which is 100% sequence identical.

 Click here to show the structure comparison results for representative 1DFU.P

 
 
  Loading...

To see how chain 1GIY.V compares with the representative chain d1dfup_ select a method below:





Entity #22: Chains: W
Description: 50S RIBOSOMAL PROTEIN L29 protein
Length: 70
No structure alignment results are available for 1GIY.W explicitly.

It is represented by chain 4HUB.V which is 100% sequence identical.

 Click here to show the structure comparison results for representative 4HUB.V

 
 
  Loading...

To see how chain 1GIY.W compares with the representative chain PDP:4HUBVa select a method below:





Entity #23: Chains: X
Description: 50S RIBOSOMAL PROTEIN L30 protein
Length: 60
No structure alignment results are available for 1GIY.X explicitly.

It is represented by chain 1BXY.A which is 100% sequence identical.

 Click here to show the structure comparison results for representative 1BXY.A

 
 
  Loading...

To see how chain 1GIY.X compares with the representative chain d1bxya_ select a method below:





Entity #3: Chains: C
Description: 50S RIBOSOMAL PROTEIN L1 protein
Length: 228
No structure alignment results are available for 1GIY.C explicitly.

It is represented by chain 3U42.A which has more than 95% sequence identity.

 Click here to show the structure comparison results for representative 3U42.A

 
 
  Loading...

To see how chain 1GIY.C compares with the representative chain PDP:3U42Aa select a method below:





Entity #4: Chains: D
Description: 50S RIBOSOMAL PROTEIN L2 protein
Length: 178
No structure alignment results are available for 1GIY.D explicitly.

It is represented by chain 1YL3.D which is 100% sequence identical.

 Click here to show the structure comparison results for representative 1YL3.D

 
 
  Loading...

To see how chain 1GIY.D compares with the representative chain d1yl3d1 select a method below:





Entity #5: Chains: E
Description: 50S RIBOSOMAL PROTEIN L3 protein
Length: 338
No structure alignment results are available for 1GIY.E explicitly.

It is represented by chain 4HUB.B which has more than 95% sequence identity.

 Click here to show the structure comparison results for representative 4HUB.B

 
 
  Loading...

To see how chain 1GIY.E compares with the representative chain PDP:4HUBBa select a method below:





Entity #6: Chains: F
Description: 50S RIBOSOMAL PROTEIN L4 protein
Length: 246
No structure alignment results are available for 1GIY.F explicitly.

It is represented by chain 4HUB.C which has more than 95% sequence identity.

 Click here to show the structure comparison results for representative 4HUB.C

 
 
  Loading...

To see how chain 1GIY.F compares with the representative chain PDP:4HUBCa select a method below:





Entity #7: Chains: G
Description: 50S RIBOSOMAL PROTEIN L5 protein
Length: 176
No structure alignment results are available for 1GIY.G explicitly.

It is represented by chain 4HUB.D which is 100% sequence identical.

 Click here to show the structure comparison results for representative 4HUB.D

 
 
  Loading...

To see how chain 1GIY.G compares with the representative chain PDP:4HUBDa select a method below:





Entity #8: Chains: H
Description: 50S RIBOSOMAL PROTEIN L6 protein
Length: 177
No structure alignment results are available for 1GIY.H explicitly.

It is represented by chain 1RL6.A which is 100% sequence identical.

 Click here to show the structure comparison results for representative 1RL6.A

 
 
  Loading...

To see how chain 1GIY.H compares with the representative chain d1rl6a1 select a method below:





Entity #9: Chains: I,J
Description: 50S RIBOSOMAL PROTEIN L7/L12 protein
Length: 128
No structure alignment results are available for 1GIY.I, 1GIY.J explicitly.

These chains are represented by chain 1DD3.A which is 100% sequence identical.

 Click here to show the structure comparison results for representative 1DD3.A

 
 
  Loading...

To see how chain 1GIY.J compares with the representative chain d1dd3a1 select a method below:





  • Update Status Hide
    Sep 16 2014

    Cluster data are up-to-date as of:
     
  • Table Legend Hide
    • Rank: current row position. Changes with different sorting orders and filter rules
    • Domain 2: Domain name of 2nd domain. Can be either a SCOP ID (d<PDB ID><Chain ID><Domain ID>), ProteinDomainParser ID (PDP:<PDB ID><Chain ID><Domain ID>)
    • Title: Protein chain description
    • P-value: P-value of this alignment (FATCAT) (default sorted by this)
    • Score: Raw alignment score (FATCAT)
    • RMSD: RMSD value of the alignment
    • Len1: Domain 1 length
    • Len2: Domain 2 length
    • %ID: % sequence identity in the alignment. A 40% sequence identity filter is applied before the structure alignments are calculated, so most results show low similarity. If the sequences are of vastly different lengths, the clustering procedure will group them in different clusters, even if they share a region of high sequence similarity.
    • %Cov1: The coverage, or %, of aligned residues in chain 1
    • %Cov2: The coverage, or %, of aligned residues in chain 2

    The table is sorting is by P-value by default. Clicking on the column header will change the sort order. Select the Filter Results lense img icon to apply other filtering criteria.

     
Comparison Tool

Calculate pairwise sequence or structure alignments.

PDB 1: Chain 1: ...
PDB 2: Chain 2: ...
Align custom files (Launches a Java Web Start application)
 

Documentation

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