Structure of PDB 5bn3 Chain A Binding Site BS01

Receptor Information

>5bn3 Chain A (length=563) Species: 228908 (Nanoarchaeum equitans Kin4-M)

MNRIISINGPLVIAKGKFSIFEVVRVGEEKLIGEVIGIENDKAYIQVYED
TNGLKVGEPVFNTGKPLTIELGPGLLANIFDGLGRPLKDIYEKTQSIYIP
KGIDLPTLDRKKVWEFIPKKKKGDTIKGGDIIGTVNENGFEHRIIVPPNV
EGKIEEIYEGNFTIEETIAIVNGKPIKLYHEWPIRKPRPYKEKLDYNYPF
ITGTRVLDIMFPIAKGGSAAVPGPFGSGKTVLNQQIAKWADSDIVIYIGC
GERGNEMTEVLEEFPKLKDPKTGKPLMYRTILIANTSNMPIAAREASIYL
GATIGEYFRDQGYSVVVNADSTSRWAEALREISSRLGEIPSEEGYPAYLL
RKLAEFYERSGRVRTLNDLEGSLTIIGAVSPPGGDFSEPVTQNTLRLVGA
LWALDSKLAYKRHYPAINYLISYTKQWEFVKKYFEELYEDVIEIREEFFA
ILKRESELMDIVSIVGALSDNEKIYLHMGRIIREGFLQQDAFDENDSYSP
LEKTIELMRIIHKYYVTVKQLLGIPLEEIEQKGIHEKIIKLRYKSLKEFR
EEIKAIEQEILSL

Ligand information

• Ligand ID: ADP
• InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: XTWYTFMLZFPYCI-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
• Formula: C10 H15 N5 O10 P2
• Name: ADENOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL14830
• DrugBank: DB16833
• ZINC: ZINC000012360703
• PDB chain: 5bn3 Chain A Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5bn3 Structural Basis for a Unique ATP Synthase Core Complex from Nanoarcheaum equitans
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): G226 G228 K229 T230 V231 Y414 Q491 D492 A493 F494
• Binding residue (residue number reindexed from 1): G226 G228 K229 T230 V231 Y414 Q489 D490 A491 F492
• Annotation score: 5

Enzymatic activity

• Catalytic site (original residue number in PDB): K229 E252 R253 K425
• Catalytic site (residue number reindexed from 1): K229 E252 R253 K425
• Enzyme Commision number: 7.1.2.2: H(+)-transporting two-sector ATPase.

Gene Ontology

Molecular Function

• GO:0005524 ATP binding
• GO:0046933 proton-transporting ATP synthase activity, rotational mechanism
• GO:0046961 proton-transporting ATPase activity, rotational mechanism

Biological Process

• GO:0006754 ATP biosynthetic process
• GO:0042777 proton motive force-driven plasma membrane ATP synthesis
• GO:0046034 ATP metabolic process
• GO:1902600 proton transmembrane transport

External links

• PDB: RCSB:5bn3, PDBe:5bn3, PDBj:5bn3
• PDBsum: 5bn3
• PubMed: 26370083
• UniProt: Q74MJ7|VATA_NANEQ V-type ATP synthase alpha chain (Gene Name=atpA)