Structure of PDB 6k3z Chain B

Receptor sequence

>6k3zB (length=1315) Species: 301447 (Streptococcus pyogenes serotype M1)

KYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLF
DSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEE
SFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRL
IYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINA
SGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFK
SNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLS
DILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFD
QSKNGYAGYIDGGASQEEFYKFIKPILEKMDTEELLVKLNREDLLRKQRT
FDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGP
LARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPN
EKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFK
TNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKIIKDK
DFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRR
RYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTF
KEDIQKAQVSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENI
VIEMARNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNG
RDMYVDQELDINRLSDYDVDAIVPQSFLKDDSIDNKVLTRSDKNRGKSDN
VPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKR
QLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKD
FQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDGKATAKY
FFYSNIMNFFKTEIKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNI
VKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVL
VVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDL
IIKLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYSP
EDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRD
KPIREQAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIH
QSITGLYETRIDLSQ

3D structure

• PDB: 6k3z Molecular basis for the PAM expansion and fidelity enhancement of an evolved Cas9 nuclease.
• Chain: B
• Resolution: 3.2 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	K33 G56 E57 T58 A59 T62 R63 R66 R69 R70 R71 Y72 R74 R75 K76 N77 Y81 L101 S104 F105 K111 R115 H116 I122 H129 I135 H160 K163 F164 R165 G166 H167 Y325 H328 H329 K336 R340 F351 F352 Y359 I363 Q402 R403 T404 F405 N407 F446 R447 I448 Y450 G453 P454 L455 A456 R457 N459 S460 F462 W464 R467 T472 I473 P475 K510 Y515 N588 R661 H721 K735 Q739 K742 K749 R753 K929 K1097 V1100 T1102 G1103 G1104 F1105 I1110 P1112 R1122 K1123 K1124 W1126 Y1131 M1169 H1349 Q1350 S1351 Y1356 E1357 T1358	K30 G53 E54 T55 A56 T59 R60 R63 R66 R67 R68 Y69 R71 R72 K73 N74 Y78 L98 S101 F102 K108 R112 H113 I119 H126 I132 H157 K160 F161 R162 G163 H164 Y322 H325 H326 K333 R337 F348 F349 Y356 I360 Q398 R399 T400 F401 N403 F442 R443 I444 Y446 G449 P450 L451 A452 R453 N455 S456 F458 W460 R463 T468 I469 P471 K506 Y511 N584 R657 H712 K726 Q730 K733 K740 R744 K910 K1053 V1056 T1058 G1059 G1060 F1061 I1066 P1068 R1078 K1079 K1080 W1082 Y1087 M1125 H1300 Q1301 S1302 Y1307 E1308 T1309
BS02	dna	B	L169 Y450 F491 I492 M495 T496 N497 K526 G582 N588 W659 R661 N692 M694 Q695 H698 R925 Q926 K1107 E1108 S1109 K1334	L166 Y446 F487 I488 M491 T492 N493 K522 G578 N584 W655 R657 N688 M690 Q691 H694 R906 Q907 K1063 E1064 S1065 K1285
BS03	dna	B	R778 K1107 R1114 D1135 S1136 K1200 S1216 Q1221 R1333 R1335	R759 K1063 R1070 D1091 S1092 K1156 S1172 Q1177 R1284 R1286

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:6k3z, PDBe:6k3z, PDBj:6k3z
• PDBsum: 6k3z
• PubMed: 31603896
• UniProt: Q99ZW2|CAS9_STRP1 CRISPR-associated endonuclease Cas9/Csn1 (Gene Name=cas9)