Structure of PDB 8em4 Chain B Binding Site BS25

Receptor Information

>8em4 Chain B (length=3818) Species: 10090 (Mus musculus)

CGSGNFRCDNGYCIPASWRCDGTRDCLDDTDEIGCPPRSCGSGFFLCPAE
GTCIPSSWVCDQDKDCSDGADEQQNCDTCGGHQFTCSNGQCINQNWVCDG
DDDCQDSGDEDGCESNQRHHTCYPREWACPGSGRCISMDKVCDGVPDCPE
GEDEYCGTGLCSILNCEYQCHQTPYGGECFCPPGHIINSNDSRTCIDFDD
CQIWGICDQKCESRQGRHQCLCEEGYILERGQHCKSNDSFSAASIIFSNG
RDLLVGDLHGRNFRILAESKNRGIVMGVDFHYQKHRVFWTDPMQAKVFST
DINGLNTQEILNVSIDAPENLAVDWINNKLYLVETRVNRIDVVNLEGNQR
VTLITENLGHPRGIALDPTVGYLFFSDWGSLSGQPKVERAFMDGSNRKDL
VTTKLGWPAGITLDLVSKRVYWVDSRYDYIETVTYDGIQRKTVARGGSLV
PHPFGISLFEEHVFFTDWTKMAVMKANKFTDTNPQVYHQSSLTPFGVTVY
HALRQPNATNPCGNNNGGCAQICVLSHRTDNGGLGYRCKCEFGFELDADE
HHCVAVKNFLLFSSQTAVRGIPFTLSTQEDVMVPVTGSPSFFVGIDFDAQ
HSTIFYSDLSKNIIYQQKIDGTGKEVITANRLQNVECLSFDWISRNLYWT
DGGSKSVTVMKLADKSRRQIISNLNNPRSIVVHPAAGYMFLSDWFRPAKI
MRAWSDGSHLMPIVNTSLGWPNGLAIDWSTSRLYWVDAFFDKIEHSNLDG
LDRKRLGHVDQMTHPFGLTVFKDNVFLTDWRLGAIIRVRKSDGGDMTVVR
RGISSIMHVKAYDADLQTGTNYCSQTTHPNGDCSHFCFPVPNFQRVCGCP
YGMKLQRDQMTCEGDPAREPPTQQCGSSSFPCNNGKCVPSIFRCDGVDDC
HDNSDEHQCGALNNTCSSSAFTCVHGGQCIPGQWRCDKQNDCLDGSDEQN
CPTRSPSSTCPPTSFTCDNHMCIPKEWVCDTDNDCSDGSDEKNCQASGTC
HPTQFRCPDHRCISPLYVCDGDKDCVDGSDEAGCVLNCTSSQFKCADGSS
CINSRYRCDGVYDCKDNSDEAGCPTRPPGMCHPDEFQCQGDGTCIPNTWE
CDGHPDCIQGSDEHNGCVPKTNQDSCLHFNGGCTHRCIQGPFGATCVCPI
GYQLANDTKTCEDVNECDIPGFCSQHCVNMRGSFRCACDPEYTLESDGRT
CKVTASENLLLVVASRDKIIMDNITAHTHNIYSLVQDVSFVVALDFDSVT
GRVFWSDLLEGKTWSAFQNGTDKRVVHDSGLSLTEMIAVDWIGRNIYWTD
YTLETIEVSKIDGSHRTVLISKNVTKPRGLALDPRMGDNVMFWSDWGHHP
RIERASMDGTMRTVIVQEKIYWPCGLSIDYPNRLIYFMDAYLDYIEFCDY
DGQNRRQVIASDLVLHHPHALTLFEDSVFWTDRGTHQVMQANKWHGRNQS
VVMYSVPQPLGIIAIHPSRQPSSPNPCASATCSHLCLLSAQEPRHYSCAC
PSGWNLSDDSVNCVRGDQPFLISVRENVIFGISLDPEVKSNDAMVPISGI
QHGYDVEFDDSEQFIYWVENPGEIHRVKTDGSNRTAFAPLSLLGSSLGLA
LDWVSRNIYYTTPASRSIEVLTLRGDTRYGKTLITNDGTPLGVGFPVGIA
VDPARGKLYWSDHGTDSGVPAKIASANMDGTSLKILFTGNMEHLEVVTLD
IQEQKLYWAVTSRGVIERGNVDGTERMILVHHLAHPWGLVVHGSFLYYSD
EQYEVIERVDKSSGSNKVVFRDNIPYLRGLRVYHHRNAADSSNGCSNNPN
ACQQICLPVPGGMFSCACASGFKLSPDGRSCSPYNSFIVVSMLPAVRGFS
LELSDHSEAMVPVAGQGRNVLHADVDVANGFIYWCDFSSSVRSSNGIRRI
KPNGSNFTNIVTYGIGANGIRGVAVDWVAGNLYFTNAFVYETLIEVIRIN
TTYRRVLLKVSVDMPRHIVVDPKHRYLFWADYGQKPKIERSFLDCTNRTV
LVSEGIVTPRGLAVDHDTGYIYWVDDSLDIIARIHRDGGESQVVRYGSRY
PTPYGITVFGESIIWVDRNLRKVFQASKQPGNTDPPTVIRDSINLLRDVT
IFDEHVQPLSPAELNNNPCLQSNGGCSHFCFALPELPTPKCGCAFGTLED
DGKNCATSREDFLIYSLNNSLRSLHFDPQDHNLPFQAISVEGMAIALDYD
RRNNRIFFTQKLNPIRGQISYVNLYSGASSPTILLSNIGVTDGIAFDWIN
RRIYYSDFSNQTINSMAEDGSNRAVIARVSKPRAIVLDPCRGYMYWTDWG
TNAKIERATLGGNFRVPIVNTSLVWPNGLTLDLETDLLYWADASLQKIER
STLTGSNREVVISTAFHSFGLTVYGQYIYWTDFYTKKIYRANKYDGSDLI
AMTTRLPTQPSGISTVVKTQQQQCSNPCDQFNGGCSHICAPGPNGAECQC
PHEGSWYLANDNKYCVVDTGARCNQFQFTCLNGRCISQDWKCDNDNDCGD
GSDELPTVCAFHTCRSTAFTCANGRCVPYHYRCDFYNDCGDNSDEAGCLF
CRDDQFTCQNGQCITKLYVCDEDNDCGDGSDEQEHLCHTPEPTCPPHQFR
CDNGHCIEMGTVCNHVDDCSDNSDEKGCGINECQDSSISHCDHNCTDTIT
SFYCSCLPGYKLMSDKRTCVDIDECKETPQLCSQKCENVIGSYICKCAPG
YIREPDGKSCRQNSNIEPYLVFSNRYYIRNLTIDGTSYSLILQGLGNVVA
LDFDRVEERLYWIDAEKQIIERMFLNKTNQETIISHRLRRAESLAVDWVS
RKLYWLDAILDCLFVSDLEGRQRKMLAQHCVDANNTFCFENPRGIVLHPQ
RGYVYWADWGDHAYIARIGMDGTNKTVIISTKIEWPNAITIDYTNDLLYW
ADAHLGYIEFSDLEGHHRHTVYDGTLPHPFALTIFEDTVFWTDWNTRTVE
KGNKYDGSGRVVLVNTTHKPFDIHVLHPYRQPIMSNPCATNNGGCSHLCL
IKAGGRGFTCECPDDFQTVQLRDRTLCMPMCSSTQFLCGNNEKCIPIWWK
CDGQKDCSDGSDESDLCPHRFCRLGQFQCRDGNCTSPQALCNARQDCADG
SDEDRVLCEHHRCEANEWQCANKRCIPEYWQCDSVDDCLDNSDEDPSHCA
SRTCRPGQFKCNNGRCIPQSWKCDVDNDCGDYSDEPIHECMTAAYNCDNH
TEFSCKTNYRCIPQWAVCNGFDDCRDNSDEQGCESVPCHPSGDFRCGNHH
CIPLRWKCDGIDDCGDNSDEESCVPRECTESEFRCADQQCIPSRWVCDQE
NDCGDNSDERDCEMKTCHPEHFQCTSGHCVPKALACDGRADCLDASDESA
CPTRFPNGTYCPAAMFECKNHVCIQSFWICDGENDCVDGSDEEIHLCCRP
GFKPSTLDKNSCQDINECEEFGICPQSCRNSKGSYECFCVDGFKSMSTHY
GERCAADGSPPLLLLPENVRIRKYNISSEKFSEYLEEEEHIQAIDYDWDP
EGIGLSVVYYTVLSQGSQFGAIKRAYLPDFESGSNNPVREVDLGLKYLMQ
PDGLAVDWVGRHIYWSDAKSQRIEVATLDGRYRKWLITTQLDQPAAIAVN
PKLGLMFWTDQGKQPKIESAWMNGEHRSVLASANLGWPNGLSIDYLNGDR
IYWSDSKEDVIESIKYDGTDRRLIINDAMKPFSLDIFEDQLYWVAKEKGE
VWRQNKFGKGNKEKLLVVNPWLTQVRIFHQLRYNQSVSNPCKQVCSHLCL
LRPGGYSCACPQGSDFVTGSTVECDAASELPITMPSPCRCMHGGSCYFDE
NDLPKCKCSSGYSGEYCE

Ligand information

• Ligand ID: CA
• InChI: InChI=1S/Ca/q+2
• InChIKey: BHPQYMZQTOCNFJ-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Ca++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Ca+2]
• Formula: Ca
• Name: CALCIUM ION
• DrugBank: DB14577
• PDB chain: 8em4 Chain B Residue 4763

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8em4 Structures of LRP2 reveal a molecular machine for endocytosis.
• Resolution: 2.83 Å
• Binding residue (original residue number in PDB): W3613 Q3614 D3616 V3618 D3620 D3626 E3627
• Binding residue (residue number reindexed from 1): W3130 Q3131 D3133 V3135 D3137 D3143 E3144
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0005509 calcium ion binding

External links

• PDB: RCSB:8em4, PDBe:8em4, PDBj:8em4
• PDBsum: 8em4
• PubMed: 36750096
• UniProt: A2ARV4|LRP2_MOUSE Low-density lipoprotein receptor-related protein 2 (Gene Name=Lrp2)