Structure of PDB 8iwr Chain A Binding Site BS02

Receptor Information

>8iwr Chain A (length=893) Species: 9606 (Homo sapiens)

MIPVLTSKKASELPVSEVASILQADLQNGLNKCEVSHRRAFHGWNEFDIS
EDEPLWKKYISQFKNPLIMLLLASAVISVLMHQFDDAVSITVAILIVVTV
AFVQEYRSEKSLEELSKLVPPECHCVREGKLEHTLARDLVPGDTVCLSVG
DRVPADLRLFEAVDLSIDESSLTGETTPCSKVTAPQPAATNGDLASRSNI
AFMGTLVRCGKAKGVVIGTGENSEFGEVFKMMQAEEAPKTPLQKSMDLLG
KQLSFYSFGIIGIIMLVGWLLGKDILEMFTISVSLAVAAIPEGLPIVVTV
TLALGVMRMVKKRAIVKKLPIVETLGCCNVICSDKTGTLTKNEMTVTHIF
TSDGLHAEVTGVGYNQFGEVIVDGDVVHGFYNPAVSRIVEAGCVCNDAVI
RNNTLMGKPTEGALIALAMKMGLDGLQQDYIRKAEYPFSSEQKWMAVKCV
HRTQQDRPEICFMKGAYEQVIKYCTTYQSKGQTLTLTQQQRDVYQQEKAR
MGSAGLRVLALASGPELGQLTFLGLVGIIDPPRTGVKEAVTTLIASGVSI
KMITGDSQETAVAIASRLGLYSKTSQSVSGEEIDAMDVQQLSQIVPKVAV
FYRASPRHKMKIIKSLQKNGSVVAMTGDGVNDAVALKAADIGVAMGQTGT
DVCKEAADMILVDDDFQTIMSAIEEGKGIYNNIKNFVRFQLSTSIAALTL
ISLATLMNFPNPLNAMQILWINIIMDGPPAQSLGVEPVDKDVIRKPPRNW
KDSILTKNLILKILVSSIIIVCGTLFVFWRELRDNVITPRDTTMTFTCFV
FFDMFNALSSRSQTKSVFEIGLCSNRMFCYAVLGSIMGQLLVIYFPPLQK
VFQTESLSILDLLFLLGLTSSVCIVAEIIKKVERSREKIQKHV

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: 8iwr Chain A Residue 1003

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8iwr Structure and transport mechanism of the human calcium pump SPCA1.
• Resolution: 3.52 Å
• Binding residue (original residue number in PDB): T352 F454 K480 R523 L525 T570 G571
• Binding residue (residue number reindexed from 1): T336 F438 K464 R507 L509 T554 G555
• 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:8iwr, PDBe:8iwr, PDBj:8iwr
• PDBsum: 8iwr
• PubMed: 37258749
• UniProt: P98194|AT2C1_HUMAN Calcium-transporting ATPase type 2C member 1 (Gene Name=ATP2C1)