Structure of PDB 6jfu Chain A

Receptor sequence

>6jfuA (length=884) Species: 487 (Neisseria meningitidis)

NPINYILGLAIGIASVGWAMVEIDEEENPIRLIDLGVRVFERAEVPKTGD
SLAMARRLARSVRRLTRRRAHRLLRARRLLKREGVLQAADFDENGLIKSL
PNTPWQLRAAALDRKLTPLEWSAVLLHLIKHRGYLSQRKNEGETADKELG
ALLKGVANNAHALQTGDFRTPAELALNKFEKESGHIRNQRGDYSHTFSRK
DLQAELILLFEKQKEFGNPHVSGGLKEGIETLLMTQRPALSGDAVQKMLG
HCTFEPAEPKAAKNTYTAERFIWLTKLNNLRILEQGSERPLTDTERATLM
DEPYRKSKLTYAQARKLLGLEDTAFFKGLREASTLMEMKAYHAISRALEK
EGLKDKKSPLNLSSELQDEIGTAFSLFKTDEDITGRLKDRVQPEILEALL
KHISFDKFVQISLKALRRIVPLMEQGKRYDEACAEIYGDHYGKKNTEEKI
YLPPIPADEIRNPVVLRALSQARKVINGVVRRYGSPARIHIETAREVGKS
FKDRKEIEDTRYVNRFLCQFVADHIVFASNGQITNLLRGKVRAENDRHHA
LDAVVVACSTVAMQQKITRFVRYKTHFPQPWEFFAQEVMIRVFGKPDGKP
EFEEADTPEKLRTLLAEKLPEAVHEYVTPLFVSRAPNRKMSGAHKDTLRS
AKRFVKHNEKISVKRVWLTEIKLADLENMVNYKNGREIELYEALKARLEA
YGGNAKQAFDPKDNPFYKKGGQLVKAVRVEKTQESGVLLNKKNAYTIADN
GDMVRVDVFCKVDKKGKNQYFIVPIYAWQVAENILPDIDCKGYRIDDSYT
FCFSLHKYDLIAFQKDEKSKVEFAYYINCDSSNGRFYLAWHDKGSKEQQF
RISTQNLVLIQKYQVNELGKEIRPCRLKKRPPVR

3D structure

• PDB: 6jfu Structures of Neisseria meningitidis Cas9 Complexes in Catalytically Poised and Anti-CRISPR-Inhibited States.
• Chain: A
• Resolution: 3.2 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	A	S57 L58 A59 R62 R63 A65 R66 R69 R70 L71 R74 H77 R81 N108 P110 W111 H133 K136 H137 R138 G139 H191 I192 R193 N194 Q195 G197 R243 P244 A245 T259 K269 Q422 Y441 Y463 P466 R479 K511 R675 R746 R836 K837 M838 S839 G840 A841 H842 L846 R847 S848 R863 W865 V878 N879 R884 E885 K916 K917 Q920 L921 K923 A924 R926 N938 A942 T944 R953 A979 E980 C1073 R1074 P1080	S51 L52 A53 R56 R57 A59 R60 R63 R64 L65 R68 H71 R75 N102 P104 W105 H127 K130 H131 R132 G133 H185 I186 R187 N188 Q189 G191 R237 P238 A239 T253 K263 Q410 Y429 Y451 P454 R467 K499 R515 R572 R638 K639 M640 S641 G642 A643 H644 L648 R649 S650 R665 W667 V680 N681 R686 E687 K718 K719 Q722 L723 K725 A726 R728 N740 A744 T746 R755 A781 E782 C875 R876 P882
BS02	dna	A	Y140 R144 K145 G156 L158 L159 Y199 L246 M254 L255 G256 K266 N285 R287 K333 D418 F420 D442 I472 T670 R675 K843 D844 T845 K870 R1033 I1050 T1052 N1054	Y134 R138 K139 G150 L152 L153 Y193 L240 M248 L249 G250 K260 N279 R281 K327 D406 F408 D430 I460 T510 R515 K645 D646 T647 K672 R835 I852 T854 N856
BS03	dna	A	T930 N948 D950 M951 Y974 N1026 D1028 S1029 S1030	T732 N750 D752 M753 Y776 N828 D830 S831 S832

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Tue Nov 26 05:10:53 2024

A problem occurred in a Python script. Here is the sequence of function calls leading up to the error, in the order they occurred.

 /var/www/html/BioLiP/pdb.cgi in <module>()

   1443                 pubmed=display_regular_ligand(pdbid,asym_id,lig3,ligIdx,title)

   1444         else:

=> 1445             pubmed,uniprot=display_protein_receptor(pdbid,asym_id,title)

   1446     

   1447     uniprot_line=''

pubmed = '', uniprot = '', display_protein_receptor = <function display_protein_receptor>, pdbid = '6jfu', asym_id = 'A', title = 'Structures of Neisseria meningitidis Cas9 Comple...ytically Poised and Anti-CRISPR-Inhibited States.'

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='6jfu', asym_id='A', title='Structures of Neisseria meningitidis Cas9 Comple...ytically Poised and Anti-CRISPR-Inhibited States.')

    839 

    840     if go:

=>  841         display_go(go,uniprot,pdbid,asym_id)

    842     return pubmed,uniprot

    843 

global display_go = <function display_go>, go = '0003676,0004519', uniprot = '', pdbid = '6jfu', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003676,0004519', uniprot='', pdbid='6jfu', asym_id='A')

    480         '''.replace("$namespace_link",namespace_link

    481           ).replace("$namespace",namespace

=>  482           ).replace("$uniprot",u

    483         ))

    484         for l,(term,name) in enumerate(go2aspect[Aspect]):

u undefined

UnboundLocalError: local variable 'u' referenced before assignment
      args = ("local variable 'u' referenced before assignment",)
      with_traceback = <built-in method with_traceback of UnboundLocalError object>