Structure of PDB 2y4k Chain B Binding Site BS01

Receptor Information
>2y4k Chain B (length=378) Species: 518766 (Rhodothermus marinus DSM 4252) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLVVFPFKHEHPEVLLHNVRVAAAHPRVHEVLCIGYERDQTYEAVERAAP
EISRATGTPVSVRLQERLGTLRPGKGDGMNTALRYFLEETQWERIHFYDA
DITSFGPDWITKAEEAADFGYGLVRHYFPRASTDAMITWMITRTGFALLW
PHTELSWIEQPLGGELLMRREVAAMLYEDERVRRRSDWGIDTLYTFVTVA
AGVSIYECYIPEGKAYGGLDDLRTMLVECFAAIQSLQHEVVGQPAIHRQE
HPHRVPVHIAERVGYDVEATLHRLMQHWTPRQVELLELFTTPVREGLRTC
QRRPAFNFMDEMAWAATYHVLLEHFQPGDPDWEELLFKLWTTRVLNYTMT
VALRGYDYAQQYLYRMLGRYRYQAALEN
Ligand information
Ligand IDGDP
InChIInChI=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
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=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 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(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
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain2y4k Chain B 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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PDB2y4k Substrate and Metal Ion Promiscuity in Mannosylglycerate Synthase.
Resolution2.45 Å
Binding residue
(original residue number in PDB)		P7 F8 K9 E11 Y37 Q66 G75 K76 D100 A101 D102 W189
Binding residue
(residue number reindexed from 1)		P6 F7 K8 E10 Y36 Q65 G74 K75 D99 A100 D101 W188
Annotation score4
Enzymatic activity
Enzyme Commision number 2.4.1.217: mannosyl-3-phosphoglycerate synthase.
Gene Ontology
Molecular Function
GO:0046872 metal ion binding

View graph for
Molecular Function
External links
PDB RCSB:2y4k, PDBe:2y4k, PDBj:2y4k
PDBsum2y4k
PubMed21288903
UniProtD0MI02

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