Structure of PDB 7yag Chain A Binding Site BS01

Receptor Information

>7yag Chain A (length=876) Species: 9606 (Homo sapiens)

VLTSKKASELPVSEVASILQADLQNGLNKCEVSHRRAFHGWNEFDISPLW
KKYISQFKNPLIMLLLASAVISVLMHQFDDAVSITVAILIVVTVAFVQEY
RSEKSLEELSKLVPPECHCVREGKLEHTLARDLVPGDTVCLSVGDRVPAD
LRLFEAVDLSIDESSLTGETTPCSKVTAPQPAASRSNIAFMGTLVRCGKA
KGVVIGTGENSEFGEVFKMMQAEEAPKTPLQKSMDLLGKQLSFYSFGIIG
IIMLVGWLLGKDILEMFTISVSLAVAAIPEGLPIVVTVTLALGVMRMVKK
RAIVKKLPIVETLGCCNVICSDKTGTLTKNEMTVTHIFTSDGLHAEVTGV
GYNQFGEVIVDGDVVHGFYNPAVSRIVEAGCVCNDAVIRNNTLMGKPTEG
ALIALAMKMGLDGLQQDYIRKAEYPFSSEQKWMAVKCVHRTQQDRPEICF
MKGAYEQVIKYCTTYQSKGQTLTLTQQQRDVYQQEKARMGSAGLRVLALA
SGPELGQLTFLGLVGIIDPPRTGVKEAVTTLIASGVSIKMITGDSQETAV
AIASRLGLYSKTSQSVSGEEIDAMDVQQLSQIVPKVAVFYRASPRHKMKI
IKSLQKNGSVVAMTGDGVNDAVALKAADIGVAMGQTGTDVCKEAADMILV
DDDFQTIMSAIEEGKGIYNNIKNFVRFQLSTSIAALTLISLATLMNFPNP
LNAMQILWINIIMDGPPAQSLGVEPVDKDVIRKPPRNWKDSILTKNLILK
ILVSSIIIVCGTLFVFWRELRDNVITPRDTTMTFTCFVFFDMFNALSSRS
QTKSVFEIGLCSNRMFCYAVLGSIMGQLLVIYFPPLQKVFQTESLSILDL
LFLLGLTSSVCIVAEIIKKVERSREK

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: 7yag Chain A Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7yag Cryo-EM structures of human SPCA1a reveal the mechanism of Ca 2+ /Mn 2+ transport into the Golgi apparatus.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): T352 E427 F454 S456 K459 K480 R523 L525 T570 G571 R619
• Binding residue (residue number reindexed from 1): T324 E399 F426 S428 K431 K452 R495 L497 T542 G543 R591
• Annotation score: 3

Enzymatic activity

• Enzyme Commision number: 7.2.2.10: P-type Ca(2+) transporter.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0005215 transporter activity
• GO:0005388 P-type calcium transporter activity
• GO:0005524 ATP binding
• GO:0016887 ATP hydrolysis activity
• GO:0046872 metal ion binding
• GO:0140613 P-type manganese transporter activity

Biological Process

• GO:0006816 calcium ion transport
• GO:0006828 manganese ion transport
• GO:0006874 intracellular calcium ion homeostasis
• GO:0008544 epidermis development
• GO:0016339 calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules
• GO:0030036 actin cytoskeleton organization
• GO:0032468 Golgi calcium ion homeostasis
• GO:0032472 Golgi calcium ion transport
• GO:0042998 positive regulation of Golgi to plasma membrane protein transport
• GO:0043123 positive regulation of canonical NF-kappaB signal transduction
• GO:0070588 calcium ion transmembrane transport
• GO:0071421 manganese ion transmembrane transport
• GO:0098629 trans-Golgi network membrane organization

Cellular Component

• GO:0000139 Golgi membrane
• GO:0005783 endoplasmic reticulum
• GO:0005794 Golgi apparatus
• GO:0005802 trans-Golgi network
• GO:0005886 plasma membrane
• GO:0016020 membrane
• GO:0032580 Golgi cisterna membrane
• GO:0033106 cis-Golgi network membrane

External links

• PDB: RCSB:7yag, PDBe:7yag, PDBj:7yag
• PDBsum: 7yag
• PubMed: 36867705
• UniProt: P98194|AT2C1_HUMAN Calcium-transporting ATPase type 2C member 1 (Gene Name=ATP2C1)