Structure of PDB 8sey Chain B Binding Site BS01

Receptor Information

>8sey Chain B (length=626) Species: 9986 (Oryctolagus cuniculus)

NFSKAMSVAKQVFNSLTEYIQGPCTGNQQSLAHSRLWDAVVGFLHVFAHM
MMKLAQDSSQIELLKELLDLQKDMVVMLLSLLEGNVVNGMIARQMVDMLV
ESSSNVEMILKPYLGRIEIMGASRRIERIYFEISETNRAQWEMPQVKESK
RQFIFDVVNEGGEAEKMELFVSFCEDTIFEMQIAAQISEPELEVQRVKFL
NYLSRNFYTLRFLALFLAFAINFILLFYKVSDSPPNMVYYFLEESTGYME
PALWCLSLLHTLVAFLCIIGYNCLKVPLVIFKREKELARKLEFDGLYITE
QPGDDDVKGQWDRLVLNTPSFPSNYWDKFVKRKVLDKHGDIFGRERIAEL
LGMDLASLEIDVKYQIWKFGVIFTDNSFLYLGWYMVMSLLGHYNNFFFAA
HLLDIAMGVKTLRTILSSVTHNGKQLVMTVGLLAVVVYLYTVVAFNFFRK
FYNKSEDEDEPDMKCDDMMTCYLFHMYVGVRAGGGIGDEIEDPAGDEYEL
YRVVFDITFFFFVIVILLAIIQGLIIDAFGELRDQQEQVKEDMETKCFIC
GIGSDYFDTTPHGFETHTLEEHNLANYMFFLMYLINKDETEHTGQESYVW
KMYQERCWDFFPAGDCFRKQYEDQLS

Ligand information

• Ligand ID: ADN
• InChI: InChI=1S/C10H13N5O4/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(18)6(17)4(1-16)19-10/h2-4,6-7,10,16-18H,1H2,(H2,11,12,13)/t4-,6-,7-,10-/m1/s1
• InChIKey: OIRDTQYFTABQOQ-KQYNXXCUSA-N
• SMILES:
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO)[CH](O)[CH]3O
  ACDLabs 10.04: n2c1c(ncnc1n(c2)C3OC(C(O)C3O)CO)N
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CO)O)O)N
• Formula: C10 H13 N5 O4
• Name: ADENOSINE
• ChEMBL: CHEMBL477
• DrugBank: DB00640
• ZINC: ZINC000002169830
• PDB chain: 8sey Chain B Residue 5101

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8sey Allosteric modulation of ryanodine receptor RyR1 by nucleotide derivatives.
• Resolution: 2.99 Å
• Binding residue (original residue number in PDB): M4954 C4958 F4959 H4983
• Binding residue (residue number reindexed from 1): M543 C547 F548 H572
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0005216 monoatomic ion channel activity
• GO:0005219 ryanodine-sensitive calcium-release channel activity
• GO:0005245 voltage-gated calcium channel activity
• GO:0005262 calcium channel activity
• GO:0005509 calcium ion binding
• GO:0005515 protein binding
• GO:0005516 calmodulin binding
• GO:0005524 ATP binding
• GO:0015278 intracellularly gated calcium channel activity
• GO:0015643 toxic substance binding
• GO:0035381 ATP-gated ion channel activity
• GO:0042802 identical protein binding
• GO:0044325 transmembrane transporter binding
• GO:0046872 metal ion binding
• GO:0097718 disordered domain specific binding

Biological Process

• GO:0003151 outflow tract morphogenesis
• GO:0006811 monoatomic ion transport
• GO:0006816 calcium ion transport
• GO:0006874 intracellular calcium ion homeostasis
• GO:0006936 muscle contraction
• GO:0006941 striated muscle contraction
• GO:0014808 release of sequestered calcium ion into cytosol by sarcoplasmic reticulum
• GO:0019722 calcium-mediated signaling
• GO:0043588 skin development
• GO:0043931 ossification involved in bone maturation
• GO:0048741 skeletal muscle fiber development
• GO:0051209 release of sequestered calcium ion into cytosol
• GO:0051289 protein homotetramerization
• GO:0055085 transmembrane transport
• GO:0070588 calcium ion transmembrane transport
• GO:0071277 cellular response to calcium ion
• GO:0071313 cellular response to caffeine

Cellular Component

• GO:0005790 smooth endoplasmic reticulum
• GO:0014802 terminal cisterna
• GO:0016020 membrane
• GO:0016529 sarcoplasmic reticulum
• GO:0030018 Z disc
• GO:0031090 organelle membrane
• GO:0033017 sarcoplasmic reticulum membrane
• GO:0034704 calcium channel complex
• GO:0042383 sarcolemma
• GO:1990425 ryanodine receptor complex

External links

• PDB: RCSB:8sey, PDBe:8sey, PDBj:8sey
• PDBsum: 8sey
• PubMed: 37192614
• UniProt: P11716|RYR1_RABIT Ryanodine receptor 1 (Gene Name=RYR1)