Structure of PDB 6k4s Chain B

Receptor sequence

>6k4sB (length=1308) Species: 301447 (Streptococcus pyogenes serotype M1)

KKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALL
FDSGETAEATRLKRTARRRYTRRKNRILYLQEIFSNEMAKVDDSFFHRLE
ESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLR
LIYLALAHMIKFRGHFLIEGDLNPDNVDKLFIQLVQTYNQLFEENPINAS
GVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKS
NFDLAEDTKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSD
ILRVNTEITKAPLSASMIKLYDEHHQDLTLLKALVRQQLPEKYKEIFFDQ
SKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRT
FDNGIIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGP
LARGNSRFAWMTRKSEETITPWNFEKVVDKGASAQSFIERMTNFDKNLPN
EKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGDQKKAIVDLLFK
TNRKVTVKQLKEDYFKKIEEFDSVEISGVEDRFNASLGTYHDLLKIIKDK
DFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRR
RYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFIQLIHDDSLTF
KEDIQKAQSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIV
IEMARSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLGRDMY
VDQELDINRLSDYDVDAIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSE
EVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVE
TRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKDFQFY
KVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDGKATAKYFFYS
NIMNFFKTEITKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKK
TEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVA
KVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIK
LPKYSLFELENGRKRMLASAGVLQKGNELALPSKYVNFLYLASHNEQKQL
FVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAE
NIIHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYE
TRIDLSQL

3D structure

• PDB: 6k4s Molecular basis for the PAM expansion and fidelity enhancement of an evolved Cas9 nuclease.
• Chain: B
• Resolution: 3.01 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 L35 G56 E57 T58 A59 T62 R63 K65 R66 R69 R70 R71 Y72 R74 R75 K76 N77 Y81 L101 S104 F105 L106 K111 R115 H116 V126 H129 I135 H160 K163 R165 G166 Y325 H328 H329 K336 R340 F351 F352 Y359 A360 I363 K401 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 F693 H721 K735 K742 R753 K929 E1099 V1100 T1102 G1103 G1104 F1105 I1110 P1112 K1113 R1122 K1123 K1124 W1126 K1130 Y1131 M1169 H1349 Q1350 Y1356 E1357 T1358	K31 L33 G54 E55 T56 A57 T60 R61 K63 R64 R67 R68 R69 Y70 R72 R73 K74 N75 Y79 L99 S102 F103 L104 K109 R113 H114 V124 H127 I133 H158 K161 R163 G164 Y321 H324 H325 K332 R336 F347 F348 Y355 A356 I359 K397 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 F689 H711 K725 K732 R743 K906 E1052 V1053 T1055 G1056 G1057 F1058 I1063 P1065 K1066 R1075 K1076 K1077 W1079 K1083 Y1084 M1122 H1292 Q1293 Y1299 E1300 T1301
BS02	dna	B	L169 Y450 F491 I492 M495 T496 N497 K526 G582 N588 N692 I694 A728 R925 Q926 K1107 E1108 S1109 K1334 R1335	L167 Y446 F487 I488 M491 T492 N493 K522 G578 N584 N688 I690 A718 R902 Q903 K1060 E1061 S1062 K1277 R1278
BS03	dna	B	R1114 S1116 K1118 D1135 S1136 A1215 S1216 V1219 R1333	R1067 S1069 K1071 D1088 S1089 A1168 S1169 V1172 R1276

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:6k4s, PDBe:6k4s, PDBj:6k4s
• PDBsum: 6k4s
• PubMed: 31603896
• UniProt: Q99ZW2|CAS9_STRP1 CRISPR-associated endonuclease Cas9/Csn1 (Gene Name=cas9)