Structure of PDB 7z4d Chain B

Receptor sequence

>7z4dB (length=1259) Species: 1314 (Streptococcus pyogenes)

DKKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGAL
LFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRL
EESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADL
RLIYLALAHMIKFRGHFLIEGDLNPDNSVDKLFIQLVQTYNQLFEENPIN
ASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNF
KSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILL
SDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFF
DQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQ
RTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYV
GPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNL
PNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLL
FKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKIIK
DKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLK
RRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSL
TFKEDIQKAQVSGQDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGR
HKPENIVIEMAAIVPQSFLKDDSIDNSDNVPSEEVVKKTQRKFDNLTKAS
ELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLK
SKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFV
YGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRK
RPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKES
ILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKS
VKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENG
RKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFV
EQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENI
IHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETR
IDLSQLGGD

3D structure

• PDB: 7z4d R-loop formation and conformational activation mechanisms of Cas9.
• Chain: B
• 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	B	K31 L35 E57 T58 A59 T62 R63 K65 R66 R69 R70 R71 Y72 R74 R75 K76 N77 L101 S104 F105 K111 R115 H116 I122 V126 H129 T134 I135 H160 K163 F164 R165 G166 H167 Y325 H328 H329 K336 R340 F351 F352 Y359 I363 K401 Q402 R403 T404 F405 N407 G408 F446 I448 Y450 G453 P454 L455 A456 R457 N459 S460 F462 R467 T472 I473 P475 K735 Q739 K742 R753 K1097 E1099 V1100 G1103 G1104 F1105 I1110 P1112 K1113 R1122 K1123 K1124 K1130 Y1131 M1169 H1349 Q1350 S1351 Y1356 E1357	K30 L34 E56 T57 A58 T61 R62 K64 R65 R68 R69 R70 Y71 R73 R74 K75 N76 L100 S103 F104 K110 R114 H115 I121 V125 H128 T133 I134 H159 K162 F163 R164 G165 H166 Y323 H326 H327 K334 R338 F349 F350 Y357 I361 K399 Q400 R401 T402 F403 N405 G406 F444 I446 Y448 G451 P452 L453 A454 R455 N457 S458 F460 R465 T470 I471 P473 K732 Q736 K739 R750 K988 E990 V991 G994 G995 F996 I1001 P1003 K1004 R1013 K1014 K1015 K1021 Y1022 M1060 H1240 Q1241 S1242 Y1247 E1248
BS02	dna	B	L169 K268 D269 Y450 F491 I492 M495 N497 K526 N692 M694 Q695 H698 T924 R925 Q926 H930 D1012 K1107 E1108 S1109 K1334	L168 K266 D267 Y448 F489 I490 M493 N495 K524 N690 M692 Q693 H696 T815 R816 Q817 H821 D903 K998 E999 S1000 K1225
BS03	dna	B	Y515 N588 R661 Y1010 G1011 D1012 S1116 S1136 K1200 A1215 S1216 Q1221 A1320 R1333 R1335	Y513 N586 R659 Y901 G902 D903 S1007 S1027 K1091 A1106 S1107 Q1112 A1211 R1224 R1226

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)