Structure of PDB 8kag Chain B

Receptor sequence

>8kagB (length=1346) Species: 301447 (Streptococcus pyogenes serotype M1)

DKKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGAL
LFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRL
EESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADL
RLIYLALAHMIKFRGHFLIEGDLNSDVDKLFIQLVQTYNQLFEENPINAS
GVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKS
NFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSD
ILRITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNG
YAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNG
SIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARG
NSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKVL
PLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTV
KQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKIIKDKDFLDNEE
NEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWGR
LSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKA
QVSGQLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMA
RENNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDM
YVDQELDINRLSDYDVDAIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPS
EEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLV
ETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKDFQF
YKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRKMI
AKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEI
VWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIAR
KKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERS
SFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASAGELQK
GNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEIIEQ
ISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPA
AFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGD

3D structure

• PDB: 8kag Trans-nuclease activity of Cas9 activated by DNA or RNA target binding.
• Chain: B
• Resolution: 3.88 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	D2 S29 K30 K31 L35 R40 K44 K45 N46 E57 T58 A59 E60 T62 R63 K65 R66 R69 R70 R71 Y72 R74 R75 K76 N77 R78 Y81 L101 S104 F105 H116 I122 E125 V126 H129 T134 I135 H160 F164 R165 G166 H167 F168 D273 D276 Y325 H328 K336 R340 F351 F352 Y359 A360 K401 Q402 R403 T404 F405 N407 G408 R447 I448 Y450 G453 P454 L455 A456 R457 N459 S460 P475 R494 H721 K735 Q739 K742 K749 Y981 M1089 P1090 Q1091 K1097 T1098 E1099 V1100 T1102 G1104 F1105 I1110 K1113 R1122 K1123 K1124 Y1131 F1134 E1225 L1226 A1227 Q1272 R1279 H1349 Q1350 S1351 Y1356 E1357 T1358	D1 S28 K29 K30 L34 R39 K43 K44 N45 E56 T57 A58 E59 T61 R62 K64 R65 R68 R69 R70 Y71 R73 R74 K75 N76 R77 Y80 L100 S103 F104 H115 I121 E124 V125 H128 T133 I134 H159 F163 R164 G165 H166 F167 D269 D272 Y317 H320 K328 R332 F343 F344 Y351 A352 K393 Q394 R395 T396 F397 N399 G400 R439 I440 Y442 G445 P446 L447 A448 R449 N451 S452 P467 R486 H707 K721 Q725 K728 K735 Y959 M1067 P1068 Q1069 K1075 T1076 E1077 V1078 T1080 G1082 F1083 I1088 K1091 R1100 K1101 K1102 Y1109 F1112 E1203 L1204 A1205 Q1250 R1257 H1327 Q1328 S1329 Y1334 E1335 T1336
BS02	rna	B	L169 Y450 M495 E1108	L168 Y442 M487 E1086

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