Structure of PDB 7z4l Chain B

Receptor sequence

>7z4lB (length=1337) Species: 1314 (Streptococcus pyogenes)

DKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGAL
LFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRL
EESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADL
RLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPI
NASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPN
FKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAIL
LSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIF
FDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRK
QRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYY
VGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKN
LPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDL
LFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKII
KDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQL
KRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDS
LTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVM
GRHKPENIVIEMAREKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNE
KLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSFLKDDSIDNKVLTR
SDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLS
ELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLK
SKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFV
YGDYKVYKATAKYFFYSNIMNFFKTEITIRKRPLIETNGETGEIVWDKGR
DFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDP
KKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNP
IDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNELAL
PSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEIIEQISEFSK
RVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKYFD
TTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQL

3D structure

• PDB: 7z4l R-loop formation and conformational activation mechanisms of Cas9.
• Chain: B
• Resolution: 2.54 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 L35 I43 K44 N46 G56 E57 T58 A59 T62 R63 K65 R66 R69 R70 R71 Y72 R74 R75 K76 N77 R78 Y81 L101 S104 F105 K111 R115 H116 I122 V126 H129 T134 I135 H160 K163 F164 R165 G166 Y325 H328 H329 K336 R340 F351 F352 Y359 A360 I363 Q402 R403 T404 F405 N407 G408 F446 R447 I448 Y450 G453 P454 L455 A456 R457 N459 S460 F462 W464 R467 T472 I473 P475 N588 H721 K735 Q739 K742 K749 Y981 M1089 P1090 Q1091 K1097 E1099 V1100 T1102 G1103 G1104 F1105 I1110 L1111 P1112 K1113 R1122 K1123 K1124 W1126 K1130 Y1131 M1169 E1225 A1227 P1229 Q1272 H1349 Q1350 S1351 Y1356 T1358	K29 K32 L34 I42 K43 N45 G55 E56 T57 A58 T61 R62 K64 R65 R68 R69 R70 Y71 R73 R74 K75 N76 R77 Y80 L100 S103 F104 K110 R114 H115 I121 V125 H128 T133 I134 H159 K162 F163 R164 G165 Y324 H327 H328 K335 R339 F350 F351 Y358 A359 I362 Q401 R402 T403 F404 N406 G407 F445 R446 I447 Y449 G452 P453 L454 A455 R456 N458 S459 F461 W463 R466 T471 I472 P474 N587 H720 K734 Q738 K741 K748 Y972 M1061 P1062 Q1063 K1069 E1071 V1072 T1074 G1075 G1076 F1077 I1082 L1083 P1084 K1085 R1094 K1095 K1096 W1098 K1102 Y1103 M1141 E1197 A1199 P1201 Q1244 H1321 Q1322 S1323 Y1328 T1330
BS02	dna	B	Y450 F491 I492 M495 N497 E584 R661 A728 R778 K782 R895 D898 K902 R905 R925 Q926 H930 K1107 E1108 S1109	Y449 F490 I491 M494 N496 E583 R660 A727 R769 K773 R886 D889 K893 R896 R916 Q917 H921 K1079 E1080 S1081
BS03	dna	B	R1114 S1116 K1118 D1135 S1136 K1200 A1215 S1216 Q1221 A1320 R1333 R1335	R1086 S1088 K1090 D1107 S1108 K1172 A1187 S1188 Q1193 A1292 R1305 R1307

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• 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:7z4l, PDBe:7z4l, PDBj:7z4l
• PDBsum: 7z4l
• PubMed: 36002571
• UniProt: Q99ZW2|CAS9_STRP1 CRISPR-associated endonuclease Cas9/Csn1 (Gene Name=cas9)