Puzzle 2657b protein does not match description

[grogar7]

The aa sequence quoted in the puzzle description still does not match what the puzzle shows. The sequence in the puzzle description starts with RNII. The actual puzzle begins with DKFD.

[beta_helix]

Fixed, thanks!

[LociOiling]

The posted sequences are often different than the puzzle, due to experimental issues, specifically "missing residues".

The protein in 2657b is a match for 1YK9.

For 1YK9, the FASTA sequences (Display Files -> FASTA Sequence) starts with RNII. That sequence is the input to the X-ray experiment.

The PDB file for 1YK9 (Display Files -> Legacy PDB Format (Header)) show there are missing residues at the start of the chain:

REMARK 465 MISSING RESIDUES                                                     
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE                       
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)                
REMARK 465                                                                      
REMARK 465   M RES C SSSEQI                                                     
REMARK 465     ARG A   240                                                      
REMARK 465     ASN A   241                                                      
REMARK 465     ILE A   242                                                      
REMARK 465     ILE A   243                                                      
REMARK 465     ALA A   244   

So the starting RNIIA residues are missing in the experimental output, and the puzzle protein ends up starting with DKFD, as noted.

It seems pretty common for the ends of a chain to not show up on the x-rays. Sometimes there are mid-chain gaps as well. Unfortunately, the rscb.org site doesn't show the output sequence. So digging into the PDB file is the only way to be sure.