Structure of PDB 8cqb Chain B Binding Site BS01

Receptor Information

>8cqb Chain B (length=478) Species: 9606 (Homo sapiens)

HMTGPMCLIENTNGRLMANPEALKILSAITQPMVVVAIVGLYRTGKSYLM
NKLAGKKKGFSLGSTVQSHTKGIWMWCVPHPKKPGHILVLLDTEGLGDVE
KGDNQNDSWIFALAVLLSSTFVYNSIGTINQQAMDQLYYVTELTHRIRSK
SSPDENENEVEDSADFVSFFPDFVWTLRDFSLDLEADGQPLTPDEYLTYS
LKLKKGTSQKDETFNLPRLCIRKFFPKKKCFVFDRPVHRRKLAQLEKLQD
EELDPEFVQQVADFCSYIFSNSKTKTLSGGIQVNGPRLESLVLTYVNAIS
SGDLPCMENAVLALAQIENSAAVQKAIAHYEQQMGQKVQLPTETLQELLD
LHRDSEREAIEVFIRSSFKDVDHLFQKELAAQLEKKRDDFCKQNQEASSD
RCSALLQVIFSPLEEEVKAGIYSKPGGYRLFVQKLQDLKKKYYEEPRKGI
QAEEILQTYLKSKESMTDAILQTDQTLT

Ligand information

• Ligand ID: GDP
• InChI: InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
• InChIKey: QGWNDRXFNXRZMB-UUOKFMHZSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
  CACTVS 3.385: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  CACTVS 3.385: NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 12.01: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
  OpenEye OEToolkits 1.7.6: c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
• Formula: C10 H15 N5 O11 P2
• Name: GUANOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL384759
• DrugBank: DB04315
• ZINC: ZINC000008215481
• PDB chain: 8cqb Chain B Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8cqb Cryo-EM structure of the human GBP1 dimer bound to GDP-AlF3
• Resolution: 3.7 Å
• Binding residue (original residue number in PDB): R48 G50 K51 S52 Y53 L67 G68 R183 D184 P241 L247
• Binding residue (residue number reindexed from 1): R43 G45 K46 S47 Y48 L62 G63 R178 D179 P236 L242
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 3.6.1.-
  3.6.5.-

Gene Ontology

Molecular Function

• GO:0001530 lipopolysaccharide binding
• GO:0003779 actin binding
• GO:0003924 GTPase activity
• GO:0003925 G protein activity
• GO:0004382 GDP phosphatase activity
• GO:0005515 protein binding
• GO:0005525 GTP binding
• GO:0016787 hydrolase activity
• GO:0019003 GDP binding
• GO:0019899 enzyme binding
• GO:0019955 cytokine binding
• GO:0030507 spectrin binding
• GO:0042802 identical protein binding
• GO:0042803 protein homodimerization activity
• GO:0051879 Hsp90 protein binding

Biological Process

• GO:0032703 negative regulation of interleukin-2 production
• GO:0042742 defense response to bacterium
• GO:0042832 defense response to protozoan
• GO:0045087 innate immune response
• GO:0050848 regulation of calcium-mediated signaling
• GO:0050860 negative regulation of T cell receptor signaling pathway
• GO:0051607 defense response to virus
• GO:0051715 cytolysis in another organism
• GO:0070373 negative regulation of ERK1 and ERK2 cascade
• GO:0071346 cellular response to type II interferon
• GO:0071347 cellular response to interleukin-1
• GO:0071356 cellular response to tumor necrosis factor
• GO:0072665 protein localization to vacuole
• GO:0140639 positive regulation of pyroptotic inflammatory response
• GO:0160075 non-canonical inflammasome complex assembly
• GO:1900025 negative regulation of substrate adhesion-dependent cell spreading
• GO:1903076 regulation of protein localization to plasma membrane
• GO:1903077 negative regulation of protein localization to plasma membrane

Cellular Component

• GO:0000139 Golgi membrane
• GO:0005576 extracellular region
• GO:0005737 cytoplasm
• GO:0005794 Golgi apparatus
• GO:0005829 cytosol
• GO:0005886 plasma membrane
• GO:0012506 vesicle membrane
• GO:0015629 actin cytoskeleton
• GO:0030659 cytoplasmic vesicle membrane
• GO:0031410 cytoplasmic vesicle
• GO:0106139 symbiont cell surface

External links

• PDB: RCSB:8cqb, PDBe:8cqb, PDBj:8cqb
• PDBsum: 8cqb
• UniProt: P32455|GBP1_HUMAN Guanylate-binding protein 1 (Gene Name=GBP1)