Structure of PDB 7z4d Chain E

Receptor sequence

>7z4dE (length=1166) Species: 1314 (Streptococcus pyogenes)

DKKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGAL
LFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRL
EESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADL
RLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPI
NASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPN
FKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAIL
LSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIF
FDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRK
QRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYY
VGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKN
LPNEKVLPKHSLLYEYFTVYNELTKQKKAIVDLLFLKEDYFKKIECFSLG
TYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHL
FDDKVMKQLKRRRYTGWGRLSRKLINIRDKQSGKTILDFLKSANRNFMQL
IHDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMAA
IVPQSFLKDDSIDNKSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKY
DENDKLIREVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVV
GTALIKKYPKLESEFVYGDYKVYDMIAKSEQEKYFFYSNIMNFFKTEITL
ANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQT
GGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKG
KSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYS
LFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDN
EQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPI
REQAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSI
TGLYETRIDLSQLGGD

3D structure

• PDB: 7z4d R-loop formation and conformational activation mechanisms of Cas9.
• Chain: E
• Resolution: 3.1 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	E	K30 E57 T58 A59 T62 R63 K65 R66 R69 R70 R71 Y72 R74 K76 N77 L101 S104 F105 V107 K111 R115 H116 I122 V126 H129 I135 H160 K163 F164 R165 G166 H167 Y325 H328 H329 L332 K336 R340 F351 F352 Y359 I363 K401 Q402 R403 T404 F405 N407 G408 F446 I448 Y450 G453 L455 A456 R457 N459 S460 F462 W464 R467 T472 I473 P475 H721 K735 Q739 K742 R753 K1097 E1099 V1100 G1103 G1104 F1105 I1110 P1112 K1113 R1122 K1123 K1124 W1126 K1130 Y1131 M1169 H1349 Q1350 S1351 Y1356 E1357	K29 E56 T57 A58 T61 R62 K64 R65 R68 R69 R70 Y71 R73 K75 N76 L100 S103 F104 V106 K110 R114 H115 I121 V125 H128 I134 H159 K162 F163 R164 G165 H166 Y324 H327 H328 L331 K335 R339 F350 F351 Y358 I362 K400 Q401 R402 T403 F404 N406 G407 F445 I447 Y449 G452 L454 A455 R456 N458 S459 F461 W463 R466 T471 I472 P474 H656 K670 Q674 K677 R688 K895 E897 V898 G901 G902 F903 I908 P910 K911 R920 K921 K922 W924 K928 Y929 M967 H1147 Q1148 S1149 Y1154 E1155
BS02	dna	E	L169 K268 D269 Y450 F491 I492 M495 N497 K526 R661 M694 Q695 K1107 E1108 S1109 K1334	L168 K267 D268 Y449 F490 I491 M494 N496 K525 R619 M648 Q649 K905 E906 S907 K1132
BS03	dna	E	K510 Y515 T519 R661 M694 Y1010 G1011 D1012 S1116 K1118 S1136 K1200 A1215 S1216 Q1221 A1320 R1333 R1335	K509 Y514 T518 R619 M648 Y817 G818 D819 S914 K916 S934 K998 A1013 S1014 Q1019 A1118 R1131 R1133

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:7z4d, PDBe:7z4d, PDBj:7z4d
• PDBsum: 7z4d
• PubMed: 36002571
• UniProt: Q99ZW2|CAS9_STRP1 CRISPR-associated endonuclease Cas9/Csn1 (Gene Name=cas9)