Structure of PDB 2f43 Chain B Binding Site BS03

Receptor Information

>2f43 Chain B (length=471) Species: 10116 (Rattus norvegicus)

SAAPKAGTATGQIVAVIGAVVDVQFDEGLPPILNALEVQGRESRLVLEVA
QHLGESTVRTIAMDGTEGLVRGQKVLDSGAPIKIPVGPETLGRIMNVIGE
PIDERGPIKTKQFAPIHAEAPEFIEMSVEQEILVTGIKVVDLLAPYAKGG
KIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEM
IESGVINLKDATSKVALVYGQMNEPPGARARVALTGLTVAEYFRDQEGQD
VLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQERITTTK
KGSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDP
LDSTSRIMDPNIVGSEHYDVARGVQKILQDYKSLQDIIAILGMDELSEER
ARKIQRFLSQPFQVAEVFTGHMGKLVPLKETIKGFQQILAGDYDHLPEQA
FYMVGPIEEAVAKADKLAEEH

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: 2f43 Chain B Residue 604

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2f43 Mitochondrial ATP synthase: Crystal structure of the catalytic F1 unit in a vanadate-induced transition-like state and implications for mechanism.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): G159 G161 K162 T163 V164 Y345 F418 A421 F424
• Binding residue (residue number reindexed from 1): G159 G161 K162 T163 V164 Y345 F412 A415 F418
• Annotation score: 5

Enzymatic activity

• Catalytic site (original residue number in PDB): K162 E188 R189 R356
• Catalytic site (residue number reindexed from 1): K162 E188 R189 R356
• Enzyme Commision number: 7.1.2.2: H(+)-transporting two-sector ATPase.

Gene Ontology

Molecular Function

• GO:0005509 calcium ion binding
• GO:0005524 ATP binding
• GO:0016887 ATP hydrolysis activity
• GO:0030228 lipoprotein particle receptor activity
• GO:0042288 MHC class I protein binding
• GO:0043531 ADP binding
• GO:0043532 angiostatin binding
• GO:0046933 proton-transporting ATP synthase activity, rotational mechanism
• GO:0046961 proton-transporting ATPase activity, rotational mechanism

Biological Process

• GO:0001525 angiogenesis
• GO:0001889 liver development
• GO:0006629 lipid metabolic process
• GO:0006754 ATP biosynthetic process
• GO:0006898 receptor-mediated endocytosis
• GO:0006933 negative regulation of cell adhesion involved in substrate-bound cell migration
• GO:0009631 cold acclimation
• GO:0010042 response to manganese ion
• GO:0015986 proton motive force-driven ATP synthesis
• GO:0042776 proton motive force-driven mitochondrial ATP synthesis
• GO:0043536 positive regulation of blood vessel endothelial cell migration
• GO:0046034 ATP metabolic process
• GO:0051453 regulation of intracellular pH
• GO:0098761 cellular response to interleukin-7
• GO:1901653 cellular response to peptide
• GO:1902600 proton transmembrane transport
• GO:1904643 response to curcumin
• GO:1905242 response to 3,3',5-triiodo-L-thyronine

Cellular Component

• GO:0005737 cytoplasm
• GO:0005739 mitochondrion
• GO:0005743 mitochondrial inner membrane
• GO:0005886 plasma membrane
• GO:0009986 cell surface
• GO:0016020 membrane
• GO:0031966 mitochondrial membrane
• GO:0042645 mitochondrial nucleoid
• GO:0045121 membrane raft
• GO:0045259 proton-transporting ATP synthase complex
• GO:0045261 proton-transporting ATP synthase complex, catalytic core F(1)

External links

• PDB: RCSB:2f43, PDBe:2f43, PDBj:2f43
• PDBsum: 2f43
• PubMed: 16531409
• UniProt: P10719|ATPB_RAT ATP synthase subunit beta, mitochondrial (Gene Name=Atp5f1b)