Structure of PDB 7d74 Chain G Binding Site BS01

Receptor Information
>7d74 Chain G (length=359) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKALILGGYGTRLRPLTLSTPKPLVDFCNKPILLHQVEALAAAGVDHVIL
AVSYMSQVLEKEMKAQEQRLGIRISMSHEEEPLGTAGPLALARDLLSETA
DPFFVLNSDVICDFPFQAMVQFHRHHGQEGSILVTKVEEPSKYGVVVCEA
DTGRIHRFVEKPQVFVSNKINAGMYILSPAVLQRIQLQPTSIEKEVFPIM
AKEGQLYAMELQGFWMDIGQPKDFLTGMCLFLQSLRQKQPERLCSGPGIV
GNVLVDPSARIGQNCSIGPNVSLGPGVVVEDGVCIRRCTVLRDARIRSHS
WLESCIVGWRCRVGQWVRMENVTVLGEDVIVNDELYLNGASVLPHKSIGE
SVPEPRIIM
Ligand information
Ligand IDGTP
InChIInChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXKMLYUALXHKNFT-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O14 P3
NameGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL1233147
DrugBankDB04137
ZINCZINC000060094177
PDB chain7d74 Chain G Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB7d74 Cryo-EM structures of human GMPPA-GMPPB complex reveal how cells maintain GDP-mannose homeostasis.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		L6 G8 G11 T12 R13 K23 A52 V53 S54 P83 G85
Binding residue
(residue number reindexed from 1)		L6 G7 G10 T11 R12 K22 A51 V52 S53 P82 G84
Annotation score4
Enzymatic activity
Enzyme Commision number 2.7.7.13: mannose-1-phosphate guanylyltransferase.
Gene Ontology
Molecular Function
GO:0004475 mannose-1-phosphate guanylyltransferase (GTP) activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0016740 transferase activity
GO:0016779 nucleotidyltransferase activity
GO:0046872 metal ion binding
Biological Process
GO:0006486 protein glycosylation
GO:0009058 biosynthetic process
GO:0009298 GDP-mannose biosynthetic process
GO:0019673 GDP-mannose metabolic process
GO:0061728 GDP-mannose biosynthetic process from mannose
GO:0141199 GDP-mannose biosynthetic process from glucose
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0120508 GDP-mannose pyrophosphorylase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7d74, PDBe:7d74, PDBj:7d74
PDBsum7d74
PubMed33986552
UniProtQ9Y5P6|GMPPB_HUMAN Mannose-1-phosphate guanyltransferase beta (Gene Name=GMPPB)

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