Structure of PDB 8kaj Chain F

Receptor sequence

>8kajF (length=1327) Species: 301447 (Streptococcus pyogenes serotype M1)

KYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLF
DSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEE
SFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRL
IYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINA
SDAKAILSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAED
ASKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKA
PLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDG
GASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIH
LGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWM
TRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLY
EYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLK
EDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDI
LEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRK
LINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSG
DSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARNS
RERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQE
LDINRLSDYDVDAIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVK
KMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQI
TKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKDFQFYKVRE
INNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRKMIAAKYF
FYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVL
SMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSP
TVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGY
KEVKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLY
LASHYEKLKGSPEDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANL
DKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYT
STKEVLDATLIHQSITGLYETRIDLSQ

3D structure

• PDB: 8kaj Trans-nuclease activity of Cas9 activated by DNA or RNA target binding.
• Chain: F
• Resolution: 3.42 Å

Enzymatic activity

• Enzyme Commision number: 3.1.-.-

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	F	A59 R63 R66 T67 R71 R74 S104 F105 V107 H116 I122 E125 V126 H129 F164 R165 G166 H167 R403 T404 F405 N407 G408 R447 I448 Y450 P454 F462 W464 K510 I1110 P1112 K1113 R1122 Y1131	A56 R60 R63 T64 R68 R71 S101 F102 V104 H113 I119 E122 V123 H126 F161 R162 G163 H164 R388 T389 F390 N392 G393 R432 I433 Y435 P439 F447 W449 K495 I1073 P1075 K1076 R1085 Y1094
BS02	dna	F	M495 R925 Q926 H930 K1107 E1108 S1109	M480 R898 Q899 H903 K1070 E1071 S1072
BS03	dna	F	D1135 S1136 K1200 S1216 Q1221 R1333 R1335	D1098 S1099 K1163 S1179 Q1184 R1296 R1298
BS04	rna	F	K30 K33 I43 K44 N46 E57 A59 T62 R69 R70 Y72 R74 R75 K76 S104 T134 I135 H160 K163 Y325 H328 H329 L332 K336 R340 F351 F352 Y359 I363 K401 Q402 R403 L455 A456 N459 S460 I473 P475 K742 K749 P1090 Q1091 E1099 V1100 T1102 G1103 G1104 F1105 R1122 K1123 K1124 F1134 M1169 E1225 L1226 A1227 P1229 Q1272 H1349 Q1350 S1351 Y1356 E1357	K27 K30 I40 K41 N43 E54 A56 T59 R66 R67 Y69 R71 R72 K73 S101 T131 I132 H157 K160 Y310 H313 H314 L317 K321 R325 F336 F337 Y344 I348 K386 Q387 R388 L440 A441 N444 S445 I458 P460 K725 K732 P1053 Q1054 E1062 V1063 T1065 G1066 G1067 F1068 R1085 K1086 K1087 F1097 M1132 E1188 L1189 A1190 P1192 Q1235 H1312 Q1313 S1314 Y1319 E1320

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003723 RNA binding
• GO:0004519 endonuclease activity
• GO:0004520 DNA endonuclease activity
• GO:0004527 exonuclease activity
• GO:0008408 3'-5' exonuclease activity
• GO:0046872 metal ion binding

Biological Process

• GO:0043571 maintenance of CRISPR repeat elements
• GO:0051607 defense response to virus

External links

• PDB: RCSB:8kaj, PDBe:8kaj, PDBj:8kaj
• PDBsum: 8kaj
• PubMed: 38811761
• UniProt: Q99ZW2|CAS9_STRP1 CRISPR-associated endonuclease Cas9/Csn1 (Gene Name=cas9)