Structure of PDB 8em4 Chain A

Receptor sequence
>8em4A (length=3818) Species: 10090 (Mus musculus) [Search protein sequence]
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
3D structure
PDB8em4 Structures of LRP2 reveal a molecular machine for endocytosis.
ChainA
Resolution2.83 Å
3D
structure
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Enzymatic activity
Enzyme Commision number ?
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 CA A W45 R46 D48 T50 D52 D58 E59 W18 R19 D21 T23 D25 D31 E32
BS02 CA A W85 D88 D90 D92 D98 E99 W58 D61 D63 D65 D71 E72
BS03 CA A W239 D242 D244 D246 D252 E253 W96 D99 D101 D103 D109 E110
BS04 CA A K283 V284 D286 V288 D290 D296 E297 K140 V141 D143 V145 D147 D153 E154
BS05 CA A F1042 D1045 V1047 D1049 D1055 E1056 F892 D895 V897 D899 D905 E906
BS06 CA A W1084 D1087 Q1089 D1091 D1097 E1098 W934 D937 Q939 D941 D947 E948
BS07 CA A W1127 V1128 D1130 D1132 D1134 D1140 E1141 W977 V978 D980 D982 D984 D990 E991
BS08 CA A Y1167 D1170 D1172 D1174 D1180 E1181 Y1017 D1020 D1022 D1024 D1030 E1031
BS09 CA A Y1206 D1209 V1211 D1213 D1219 E1220 Y1056 D1059 V1061 D1063 D1069 E1070
BS10 CA A W1249 D1252 H1254 D1256 D1262 E1263 W1099 D1102 H1104 D1106 D1112 E1113
BS11 CA A W2718 D2721 D2723 D2725 D2731 E2732 W2490 D2493 D2495 D2497 D2503 E2504
BS12 CA A Y2759 D2762 Y2764 N2765 D2766 D2772 E2773 Y2531 D2534 Y2536 N2537 D2538 D2544 E2545
BS13 CA A Y3051 D3054 D3056 D3058 D3064 E3065 Y2568 D2571 D2573 D2575 D2581 E2582
BS14 CA A T3094 N3097 V3099 D3101 D3107 E3108 T2611 N2614 V2616 D2618 D2624 E2625
BS15 CA A W3532 K3533 D3535 Q3537 D3539 D3545 E3546 W3049 K3050 D3052 Q3054 D3056 D3062 E3063
BS16 CA A A3572 N3575 R3577 D3579 D3585 E3586 A3089 N3092 R3094 D3096 D3102 E3103
BS17 CA A W3613 Q3614 D3616 V3618 D3620 D3626 E3627 W3130 Q3131 D3133 V3135 D3137 D3143 E3144
BS18 CA A W3654 D3657 D3659 D3661 D3667 E3668 W3171 D3174 D3176 D3178 D3184 E3185
BS19 CA A A3699 N3702 F3704 D3706 D3712 E3713 A3216 N3219 F3221 D3223 D3229 E3230
BS20 CA A W3739 D3742 I3744 D3746 D3752 E3753 W3256 D3259 I3261 D3263 D3269 E3270
BS21 CA A W3778 D3781 E3783 D3785 D3791 E3792 W3295 D3298 E3300 D3302 D3308 E3309
BS22 CA A L3817 D3820 R3822 D3824 D3830 E3831 L3334 D3337 R3339 D3341 D3347 E3348
BS23 CA A W3861 D3864 E3866 D3868 D3874 E3875 W3378 D3381 E3383 D3385 D3391 E3392
BS24 CA A D1391 V1392 E1394 N1407 M1408 G1410 S1411 D1163 V1164 E1166 N1179 M1180 G1182 S1183
BS25 CA A I3113 E3115 D3130 T3131 I3132 T3133 S3134 I2630 E2632 D2647 T2648 I2649 T2650 S2651
BS26 CA A D3154 I3155 E3157 N3171 V3172 S3175 D2671 I2672 E2674 N2688 V2689 S2692
BS27 CA A D4009 I4010 E4012 N4025 S4026 S4029 D3414 I3415 E3417 N3430 S3431 S3434
BS28 CA A S575 D578 P601 T1131 D1132 S425 D428 P451 T981 D982
BS29 CA A A888 D891 T913 A738 D741 T763
BS30 CA A A1618 D1621 H1644 A1390 D1393 H1416
BS31 CA A D2254 D2257 P2279 D2026 D2029 P2051
BS32 CA A A3291 D3294 E3323 A2808 D2811 E2840
BS33 CA A D3344 E3367 D2861 E2884
BS34 CA A D242 D244 D246 D99 D101 D103
BS35 CA A F1042 D1049 F892 D899
BS36 CA A D1130 D1134 D980 D984
BS37 CA A D3054 D3056 D2571 D2573
BS38 CA A W3613 D3616 V3618 D3620 W3130 D3133 V3135 D3137
BS39 CA A W3654 D3659 W3171 D3176
BS40 CA A E3783 D3785 E3300 D3302
Gene Ontology
Molecular Function
GO:0005509 calcium ion binding

View graph for
Molecular Function
External links
PDB RCSB:8em4, PDBe:8em4, PDBj:8em4
PDBsum8em4
PubMed36750096
UniProtA2ARV4|LRP2_MOUSE Low-density lipoprotein receptor-related protein 2 (Gene Name=Lrp2)

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