Structure of PDB 8kaj Chain B

Receptor sequence

>8kajB (length=1326) Species: 301447 (Streptococcus pyogenes serotype M1)

KYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLF
DSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEE
SFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRL
IYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINA
SGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFK
SNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLS
DILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFD
QSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQR
TFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVG
PLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLP
NEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLF
KTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKIIKD
KDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKR
RRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLT
FKEDIQKAQVSGDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHK
PENIVIEMARNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYY
LQNGRDMYVDQELDINRLSDYDVDAIVPQDDSIDNKVLTRSDKNRGKSDN
VPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKR
QLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKD
FQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDKVYDVRK
MAKYFFYSNIMNFFKTEITLKRPLIETNGETGEIVWDKGRDFATVRKVLS
MPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPT
VAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYK
EVKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYL
ASHYEKLKGSPEDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLD
KVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTS
TKEVLDATLIHQSITGLYETRIDLSQ

3D structure

• PDB: 8kaj Trans-nuclease activity of Cas9 activated by DNA or RNA target binding.
• Chain: B
• 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	B	A59 R63 R66 T67 R70 R71 R74 S104 F105 R115 H116 E125 V126 H129 F164 R165 G166 R403 T404 F405 N407 G408 R447 I448 Y450 P454 F462 E584 R661 I1110 P1112 K1113 Y1131	A56 R60 R63 T64 R67 R68 R71 S101 F102 R112 H113 E122 V123 H126 F161 R162 G163 R400 T401 F402 N404 G405 R444 I445 Y447 P451 F459 E581 R658 I1072 P1074 K1075 Y1093
BS02	dna	B	Y450 F491 M495 R925 Q926 K1107 E1108 S1109 K1334 S1338	Y447 F488 M492 R906 Q907 K1069 E1070 S1071 K1296 S1300
BS03	dna	B	K1107 R1114 S1116 K1118 S1136 K1200 S1216 Q1221 R1333 R1335	K1069 R1076 S1078 K1080 S1098 K1162 S1178 Q1183 R1295 R1297
BS04	rna	B	K30 L35 R40 K44 N46 E57 T62 R69 R70 Y72 R74 N77 Y81 L101 S104 F105 T134 I135 H160 K163 Y325 H328 H329 L332 K336 R340 F351 F352 Y359 I363 K401 Q402 R403 L455 A456 R457 N459 S460 F462 T472 I473 P475 H721 K735 Q739 K742 P1090 K1097 E1099 V1100 G1103 G1104 F1105 R1122 K1123 K1124 F1134 M1169 E1225 L1226 A1227 Q1272 H1349 Q1350 S1351 Y1356 E1357	K27 L32 R37 K41 N43 E54 T59 R66 R67 Y69 R71 N74 Y78 L98 S101 F102 T131 I132 H157 K160 Y322 H325 H326 L329 K333 R337 F348 F349 Y356 I360 K398 Q399 R400 L452 A453 R454 N456 S457 F459 T469 I470 P472 H716 K730 Q734 K737 P1052 K1059 E1061 V1062 G1065 G1066 F1067 R1084 K1085 K1086 F1096 M1131 E1187 L1188 A1189 Q1234 H1311 Q1312 S1313 Y1318 E1319

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)