Structure of PDB 6xmq Chain A Binding Site BS01

Receptor Information

>6xmq Chain A (length=1085) Species: 559292 (Saccharomyces cerevisiae S288C)

KSFVSSPIVRDSTLLVPKSLIAKPYVLPFFPLYATFAQLYFEWTFVYLGT
LVSLNILVMLMPAWNVKIKAKFNYSTTKNVNEATHILIYTTPNNGSDGIV
EIQRVTEAGSLQTFFQFQKKRFLWHENEQVFSSPKFLVDESPKIGDFQKC
KGHSGDLTHLKRLYGENSFDIPIPTFMELFKEHAVAPLFVFQVFCVALWL
LDEFWYYSLFNLFMIISMEAAAVFQRLTALKEFRTMGIKPYTINVFRNKK
WVALQTNELLPMDLVSITRTAEESAIPCDLILLDGSAIVNEAMLSGESTP
LLKESIKLRPSEDNLQLDGVDKIAVLHGGTKALQVTPPEHKSDIPPPPDG
GALAIVTKTGFETSQGSLVRVMIYSAERVSVDNKEALMFILFLLIFAVIA
SWYVWVEGTKMGRIQSKLILDCILIITSVVPPELPMELTMAVNSSLAALA
KFYVYCTEPFRIPFAGRIDVCCFDKTGTLTGEDLVFEGLAGISADSENIR
HLYSAAEAPESTILVIGAAHALVKLEDGDIVGDPMEKATLKAVGWAVERK
NSNYREGTGKLDIIRRFQFSSALKRSASIASHNDALFAAVKGAPETIRER
LSDIPKNYDEIYKSFTRSGSRVLALASKSLPKDLNRDDVESELTFNGFLI
FHCPLKDDAIETIKMLNESSHRSIMITGDNPLTAVHVAKEVGIVFGETLI
LDRAGKSDDNQLLFRDVEETVSIPFDPSKDTFDHSKLFDRYDIAVTGYAL
NALEGHSQLRDLLRHTWVYARVSPSQKEFLLNTLKDMGYQTLMCGDGTND
VGALKQAHVGIALLNGTEEGLKKLGEQRRLEASCAAPFTSKLANVSAVTN
IIRQGRCALVNTIQMYKILALNCLISAYSLSIIYMAGVKFGDGQATVSGL
LLSVCFLSISRGKPLEKLSKQRPQSGIFNVYIMGSILSQFAVHIATLVYI
TTEIYKLEPREPQVDLEKEFAPSLLNTGIFIIQLVQQVSTFAVNYQGEPF
RENIRSNKGMYYGLLGVTGLALASATEFLPELNEAMKFVPMTDDFKIKLT
LTLLLDFFGSWGVEHFFKFFFMDDKPSDISVQQVK

Ligand information

• Ligand ID: ACP
• InChI: InChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-31(24,25)28-30(22,23)4-29(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H,24,25)(H2,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1
• InChIKey: UFZTZBNSLXELAL-IOSLPCCCSA-N
• SMILES:
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)C[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)CP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)O)O)N
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(CP(=O)(O)O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O
• Formula: C11 H18 N5 O12 P3
• Name: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER;
  ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
• ChEMBL: CHEMBL133463
• DrugBank: DB03909
• ZINC: ZINC000008295124
• PDB chain: 6xmq Chain A Residue 1301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6xmq The endoplasmic reticulum P5A-ATPase is a transmembrane helix dislocase.
• Resolution: 3.7 Å
• Binding residue (original residue number in PDB): D487 T489 F582 K604 G605 R634 L636 D699 D816 N819
• Binding residue (residue number reindexed from 1): D474 T476 F569 K591 G592 R621 L623 D679 D796 N799
• Annotation score: 3

Enzymatic activity

• Enzyme Commision number: 7.4.2.-

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0005215 transporter activity
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0015662 P-type ion transporter activity
• GO:0016887 ATP hydrolysis activity
• GO:0019829 ATPase-coupled monoatomic cation transmembrane transporter activity
• GO:0046872 metal ion binding
• GO:0070273 phosphatidylinositol-4-phosphate binding
• GO:0140358 P-type transmembrane transporter activity
• GO:0140567 membrane protein dislocase activity

Biological Process

• GO:0006874 intracellular calcium ion homeostasis
• GO:0015031 protein transport
• GO:0030026 intracellular manganese ion homeostasis
• GO:0034214 protein hexamerization
• GO:0043335 protein unfolding
• GO:0055085 transmembrane transport
• GO:0055092 sterol homeostasis
• GO:0098655 monoatomic cation transmembrane transport
• GO:0140569 extraction of mislocalized protein from ER membrane

Cellular Component

• GO:0005739 mitochondrion
• GO:0005783 endoplasmic reticulum
• GO:0005789 endoplasmic reticulum membrane
• GO:0005801 cis-Golgi network
• GO:0016020 membrane

External links

• PDB: RCSB:6xmq, PDBe:6xmq, PDBj:6xmq
• PDBsum: 6xmq
• PubMed: 32973005
• UniProt: P39986|SPF1_YEAST Endoplasmic reticulum transmembrane helix translocase (Gene Name=SPF1)