Structure of PDB 2y4m Chain B Binding Site BS02

Receptor Information
>2y4m Chain B (length=380) 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
AGVSIYECYIPEGKAHRLYGGLDDLRTMLVECFAAIQSLQHEVVGQPAIH
RQEHPHRVPVHIAERVGYDVEATLHRLMQHWTPRQVELLELFTTPVREGL
RTCQRRPAFNFMDEMAWAATYHVLLEHFQPGDPDWEELLFKLWTTRVLNY
TMTVALRGYDYAQQYLYRMLGRYRYQAALE
Ligand information
Ligand IDGDX
InChIInChI=1S/C16H23N5O17P2/c17-16-19-11-4(12(27)20-16)18-2-21(11)13-8(25)5(22)3(35-13)1-34-39(30,31)38-40(32,33)37-15-9(26)6(23)7(24)10(36-15)14(28)29/h2-3,5-10,13,15,22-26H,1H2,(H,28,29)(H,30,31)(H,32,33)(H3,17,19,20,27)/t3-,5-,6+,7+,8-,9+,10+,13-,15-/m1/s1
InChIKeyDNBSDUDYNPJVCN-ZXTXFPBHSA-N
SMILES
SoftwareSMILES
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]4O[CH]([CH](O)[CH](O)[CH]4O)C(O)=O)[CH](O)[CH]3O
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[C@H]4O[C@@H]([C@@H](O)[C@H](O)[C@@H]4O)C(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)O[C@@H]4[C@H]([C@H]([C@@H]([C@H](O4)C(=O)O)O)O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.7.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OC4C(C(C(C(O4)C(=O)O)O)O)O)O)O)N=C(NC2=O)N
ACDLabs 12.01O=C4NC(=Nc1c4ncn1C2OC(C(O)C2O)COP(=O)(OP(=O)(OC3OC(C(=O)O)C(O)C(O)C3O)O)O)N
FormulaC16 H23 N5 O17 P2
NameGUANOSINE 5'-(TRIHYDROGEN DIPHOSPHATE), P'-D-MANNOPYRANOSYL ESTER
ChEMBL
DrugBankDB04023
ZINCZINC000008216635
PDB chain2y4m 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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PDB2y4m Substrate and Metal Ion Promiscuity in Mannosylglycerate Synthase.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		P7 F8 E11 Y37 Q66 G75 K76 D100 A101 D102 L163 G165 W189 D192 K215 H217 M229
Binding residue
(residue number reindexed from 1)		P6 F7 E10 Y36 Q65 G74 K75 D99 A100 D101 L162 G164 W188 D191 K214 H216 M228
Annotation score3
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:2y4m, PDBe:2y4m, PDBj:2y4m
PDBsum2y4m
PubMed21288903
UniProtD0MI02

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