Structure of PDB 8x93 Chain A Binding Site BS09

Receptor Information

>8x93 Chain A (length=1371) Species: 9606 (Homo sapiens)

VVRKYAKKITEWPPFEYMILATIIANCIVLALEQHLPDDDKTPMSERLDD
TEPYFIGIFCFEAGIKIIALGFSYLRNGWNVMDFVVVLTGILATVGTEFD
LRTLRAVRVLRPLKLVSGIPSLQVVLKSIMKAMIPLLQIGLLLFFAILIF
AIIGLEFYMGKFHTTCFEEGTDDIQGESPAPCGTEEPARTCPNGTKCQPY
WEGPNNGITQFDNILFAVLTVFQCITMEGWTDLLYNSNDASGNTWNWLYF
IPLIIIGSFFMLNLVLGVLSGEFAKERERVENRRAFLKLRRQQQIERELN
GYMEWISKAEEVILASTFFHKKERRMRFYIRRMVKTQAFYWTVLSLVALN
TLCVAIVHYNQPEWLSDFLYYAEFIFLGLFMSEMFIKMYGLGTRPYFHSS
FNCFDCGVIIGSIFEVIWAVIKPGTSFGISVLRALRLLRIFKVTKYWASL
RNLVVSLLNSMKSIISLLFLLFLFIVVFALLGMQLFGGQFNFDEGTPPTN
FDTFPAAIMTVFQILTGEDWNEVMYDGIKSQGGVQGGMVFSIYFIVLTLF
GNYTLLNVFLAIAVDNLANAQELTKDEQEEEEAANQKLALQKAKEVAEVS
NQKPAKSVWEQRTSEMRKQNLLASNPLRRLCHYILNLRYFEMCILMVIAM
SSIALAAEDPVQPNAPRNNVLRYFDYVFTGVFTFEMVIKMIDLGLVLHQG
AYFRDLWNILDFIVVSGALVAFAFTGNSKGKDINTIKSLRVLRVLRPLKT
IKRLPKLKAVFDCVVNSLKNVFNILIVYMLFMFIFAVVAVQLFKGKFFHC
TDESKEFEKDCRGKYLLYEKNEVKARDREWKKYEFHYDNVLWALLTLFTV
STGEGWPQVLKHSVDATFENQGPSPGYRMEMSIFYVVYFVVFPFFFVNIF
VALIIITFQEQGDKMMEEYSLEKNERACIDFAISAKPLTRHMPQNKQSFQ
YRMWQFVVSPPFEYTIMAMIALNTIVLMMKFYGASVAYENALRVFNIVFT
SLFSLECVLKVMAFGILNYFRDAWNIFDFVTVLGSITDILVTEFLSFLRL
FRAARLIKLLRQGYTIRILLWTFVQSFKALPYVCLLIAMLFFIYAIIGMQ
VFGNIGIDVEDEDSDEDEFQITEHNNFRTFFQALMLLFRSATGEAWHNIM
LSCLSGKPCDKNSGILTRECGNEFAYFYFVSFIFLCSFLMLNLFVAVIMD
NFEYLTRDSSILGPHHLDEYVRVWAEYDPAAWGRMPYLDMYQMLRHMSPP
LGLGKKCPARVAYKRLLRMDLPVADDNTVHFNSTLMALIRTALDIKIAKG
GADKQQMDAELRKEMMAIWPNLSQKTLDLLVTPHKSTDLTVGKIYAAMMI
MEYYRQSKAKKLQAMREEQDR

Ligand information

• Ligand ID: CLR
• InChI: InChI=1S/C27H46O/c1-18(2)7-6-8-19(3)23-11-12-24-22-10-9-20-17-21(28)13-15-26(20,4)25(22)14-16-27(23,24)5/h9,18-19,21-25,28H,6-8,10-17H2,1-5H3/t19-,21+,22+,23-,24+,25+,26+,27-/m1/s1
• InChIKey: HVYWMOMLDIMFJA-DPAQBDIFSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC(C)CCCC(C)C1CCC2C1(CCC3C2CC=C4C3(CCC(C4)O)C)C
  CACTVS 3.341: CC(C)CCC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CC=C4C[C@@H](O)CC[C@]4(C)[C@H]3CC[C@]12C
  ACDLabs 10.04: OC4CCC3(C(=CCC2C1C(C(C(C)CCCC(C)C)CC1)(C)CCC23)C4)C
  OpenEye OEToolkits 1.5.0: CC(C)CCC[C@@H](C)[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3[C@H]2CC=C4[C@@]3(CC[C@@H](C4)O)C)C
  CACTVS 3.341: CC(C)CCC[CH](C)[CH]1CC[CH]2[CH]3CC=C4C[CH](O)CC[C]4(C)[CH]3CC[C]12C
• Formula: C27 H46 O
• Name: CHOLESTEROL
• ChEMBL: CHEMBL112570
• DrugBank: DB04540
• ZINC: ZINC000003875383
• PDB chain: 8x93 Chain A Residue 2611

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8x93 Structural basis for different omega-agatoxin IVA sensitivities of the P-type and Q-type Ca v 2.1 channels.
• Resolution: 2.92 Å
• Binding residue (original residue number in PDB): N1783 E1784
• Binding residue (residue number reindexed from 1): N1172 E1173
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0001540 amyloid-beta binding
• GO:0005216 monoatomic ion channel activity
• GO:0005245 voltage-gated calcium channel activity
• GO:0005262 calcium channel activity
• GO:0005515 protein binding
• GO:0008331 high voltage-gated calcium channel activity
• GO:0019905 syntaxin binding
• GO:0046872 metal ion binding

Biological Process

• GO:0006811 monoatomic ion transport
• GO:0006816 calcium ion transport
• GO:0007204 positive regulation of cytosolic calcium ion concentration
• GO:0007268 chemical synaptic transmission
• GO:0050804 modulation of chemical synaptic transmission
• GO:0055085 transmembrane transport
• GO:0070588 calcium ion transmembrane transport
• GO:0098703 calcium ion import across plasma membrane
• GO:1904645 response to amyloid-beta
• GO:1904646 cellular response to amyloid-beta

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005886 plasma membrane
• GO:0005891 voltage-gated calcium channel complex
• GO:0016020 membrane
• GO:0034702 monoatomic ion channel complex
• GO:0042995 cell projection
• GO:0043025 neuronal cell body
• GO:0045202 synapse

External links

• PDB: RCSB:8x93, PDBe:8x93, PDBj:8x93
• PDBsum: 8x93
• PubMed: 38443561
• UniProt: O00555|CAC1A_HUMAN Voltage-dependent P/Q-type calcium channel subunit alpha-1A (Gene Name=CACNA1A)