Structure of PDB 8kal Chain B

Receptor sequence

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

KYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLF
DSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEE
SFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRL
IYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINA
SGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFK
SNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLS
DILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFD
QSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQR
TFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVG
PLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLP
NEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLF
KTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKIIKD
KDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKR
RRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLT
FKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGR
HKPENIVIEMARNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYL
YYLQNGRDMYVDQELDINRLSDYDVDAIVPQSFLKDDSIDNKVLTRSDKN
RGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDK
AGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLV
SDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDG
KATAKYFFYSNIMNFFKTEIKRPLIETNGETGEIVWDKGRDFATVRKVLS
MPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPT
VAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYK
EVKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYL
ASHYEKLKGSPEDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLD
KVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTS
TKEVLDATLIHQSITGLYETRIDLSQ

3D structure

• PDB: 8kal Trans-nuclease activity of Cas9 activated by DNA or RNA target binding.
• Chain: B
• Resolution: 3.16 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	K30 K33 I43 K44 N46 G56 E57 T58 A59 T62 R63 R66 R69 R70 R71 Y72 R74 R75 K76 N77 Y81 L101 S104 F105 K111 R115 H116 E125 V126 H129 T134 I135 F164 R165 G166 F168 Y325 H328 H329 K336 F351 Y359 A360 I363 Q402 R403 T404 F405 N407 G408 F446 R447 I448 Y450 P454 L455 A456 R457 S460 F462 W464 R467 T472 I473 P475 H721 K735 Q739 K742 Q894 M1089 P1090 Q1091 K1097 E1099 V1100 T1102 G1104 F1105 I1110 P1112 R1122 K1123 K1124 W1126 Y1131 E1225 L1226 A1227 P1229 Q1272 H1349 Q1350 Y1356	K27 K30 I40 K41 N43 G53 E54 T55 A56 T59 R60 R63 R66 R67 R68 Y69 R71 R72 K73 N74 Y78 L98 S101 F102 K108 R112 H113 E122 V123 H126 T131 I132 F161 R162 G163 F165 Y322 H325 H326 K333 F348 Y356 A357 I360 Q399 R400 T401 F402 N404 G405 F443 R444 I445 Y447 P451 L452 A453 R454 S457 F459 W461 R464 T469 I470 P472 H718 K732 Q736 K739 Q881 M1051 P1052 Q1053 K1059 E1061 V1062 T1064 G1066 F1067 I1072 P1074 R1084 K1085 K1086 W1088 Y1093 E1187 L1188 A1189 P1191 Q1234 H1311 Q1312 Y1318
BS02	dna	B	Y450 F491 M495 T496 A728 R778 D898 K902 R905 R925 Q926 K1107 E1108 S1109 K1334	Y447 F488 M492 T493 A725 R765 D885 K889 R892 R912 Q913 K1069 E1070 S1071 K1296
BS03	dna	B	S777 K1107 R1114 S1116 D1135 S1136 K1200 A1215 S1216 Q1221 R1335	S764 K1069 R1076 S1078 D1097 S1098 K1162 A1177 S1178 Q1183 R1297

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