Structure of PDB 8sqh Chain A

Receptor sequence

>8sqhA (length=1341) Species: 1314 (Streptococcus pyogenes)

KKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALL
FDSGETAERTRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLE
ESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLR
LIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPIN
ASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNF
KSNFDLAEDAKLQLSKDTYDDDLDNLLAQIDLFLAAKNLSDAILLSDILR
VNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKN
GYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDN
GSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLAR
GNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKV
LPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNR
KVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKIIKDKDFL
DNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRYT
GWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKED
IQKAQDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIE
MARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLY
LYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSFLKDDSIDNKVLTRSDK
NRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELD
KAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKL
VSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGD
YKVIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWD
KGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESIRPKRNSDKLIARKKD
WDPKKYGGFLWPTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFE
KNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASAKQLQKGNE
LALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEIIEQISE
FSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTRLGAPRAFK
YFDTTIDPKQYRSTKEVLDATLIHQSITGLYETRIDLSQLG

3D structure

• PDB: 8sqh Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9
• Chain: A
• Resolution: 3.69 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	A	K30 I43 K44 N46 E57 T58 A59 R61 T62 R63 R66 R69 R70 R71 Y72 R74 R75 K76 N77 L101 S104 F105 K111 R115 H116 I122 E125 V126 H129 T134 I135 H160 K163 F164 R165 G166 Y325 H328 H329 K336 R340 F351 F352 I363 Q402 R403 T404 F405 N407 G408 F446 R447 I448 Y450 G453 P454 L455 A456 R457 N459 S460 F462 W464 T472 I473 F491 K500 K510 Y515 N588 R661 M694 H721 S730 P731 K735 R765 S777 E779 R780 N803 K848 D850 S851 K918 R919 E1007 Y1010 Y1013 M1089 P1090 Q1091 E1099 V1100 T1102 G1103 G1104 F1105 I1110 P1112 K1113 R1122 K1123 K1124 W1126 Y1131 M1169 E1225 A1227 Q1272 H1349 Q1350 S1351 Y1356	K28 I41 K42 N44 E55 T56 A57 R59 T60 R61 R64 R67 R68 R69 Y70 R72 R73 K74 N75 L99 S102 F103 K109 R113 H114 I120 E123 V124 H127 T132 I133 H158 K161 F162 R163 G164 Y318 H321 H322 K329 R333 F344 F345 I356 Q395 R396 T397 F398 N400 G401 F439 R440 I441 Y443 G446 P447 L448 A449 R450 N452 S453 F455 W457 T465 I466 F484 K493 K503 Y508 N581 R654 M687 H709 S718 P719 K723 R753 S765 E767 R768 N791 K836 D838 S839 K906 R907 E995 Y998 Y1001 M1064 P1065 Q1066 E1074 V1075 T1077 G1078 G1079 F1080 I1085 P1087 K1088 R1097 K1098 K1099 W1101 Y1106 M1144 E1200 A1202 Q1247 H1324 Q1325 S1326 Y1331
BS02	dna	A	N863 R864 D868 K1107 E1108 S1109 R1111 K1334	N851 R852 D856 K1082 E1083 S1084 R1086 K1309
BS03	dna	A	D10 G12 T13 N14 S15 A914 G915 F916 I917 Q920 L921 R976 H983 Y1001 K1003 L1004 K1014 R1114 K1118 L1135 W1136 K1200 S1216 Q1219 Q1221 A1320 R1322 R1337	D8 G10 T11 N12 S13 A902 G903 F904 I905 Q908 L909 R964 H971 Y989 K991 L992 K1002 R1089 K1093 L1110 W1111 K1175 S1191 Q1194 Q1196 A1295 R1297 R1312
BS04	dna	A	Y450 M495 N497 G582 E584 N588 R655 T657 G658 W659 N692 M694 Q695 R765 E766 N767 Q768 T770 G773 Q774 K810 S834 D837 V838 H840 N863 R925 Q926 K929 A1032	Y443 M488 N490 G575 E577 N581 R648 T650 G651 W652 N685 M687 Q688 R753 E754 N755 Q756 T758 G761 Q762 K798 S822 D825 V826 H828 N851 R913 Q914 K917 A1007
BS05	MG	A	D10 E762	D8 E750
BS06	MG	A	D10 H983	D8 H971
BS07	MG	A	D839 N863 K866	D827 N851 K854

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:8sqh, PDBe:8sqh, PDBj:8sqh
• PDBsum: 8sqh
• PubMed: 38688943
• UniProt: Q99ZW2|CAS9_STRP1 CRISPR-associated endonuclease Cas9/Csn1 (Gene Name=cas9)