Structure of PDB 5mm0 Chain A Binding Site BS01

Receptor Information
>5mm0 Chain A (length=355) Species: 186497 (Pyrococcus furiosus DSM 3638) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FQSMKVSVIIPTYNERENLEELFSRIDNALQGLNYEIVVVDDDSPDRTWE
KAQELSSKYPVKVIRRTKEKGLSSAVIRGFKEASGDVFVVMDADLQHPPE
VIPKLIEAIKNGSDIAIGSRYVKGGKVENWPFYRKLISKGAIMVGRIALP
KIRDIKDPVSGFFALRKEVVEGVELNPIGFKILMEILIKGKYSKVVEVPF
TFGIRARGESKLKGKTIFEYLRHIYRLMKWEGEIDRIVKFSIVGLSGILV
NEGFLWLFVNLGIPKEIAVIPAVELSILNNFFWNDIWTFKDIRRGSIFSR
LLKFHIAALSGAVVNFIVYWILLFLGIHYLIANLVGIVLSFGVRYVINRH
VTWAT
Ligand information
Ligand IDGDD
InChIInChI=1S/C16H25N5O16P2/c17-16-19-12-6(13(28)20-16)18-3-21(12)14-10(26)8(24)5(34-14)2-33-38(29,30)37-39(31,32)36-15-11(27)9(25)7(23)4(1-22)35-15/h3-5,7-11,14-15,22-27H,1-2H2,(H,29,30)(H,31,32)(H3,17,19,20,28)/t4-,5-,7-,8-,9+,10-,11+,14-,15-/m1/s1
InChIKeyMVMSCBBUIHUTGJ-GDJBGNAASA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[C@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O
ACDLabs 10.04O=P(OC1OC(C(O)C(O)C1O)CO)(O)OP(=O)(O)OCC4OC(n2c3N=C(N)NC(=O)c3nc2)C(O)C4O
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OC4C(C(C(C(O4)CO)O)O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(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)CO)O)O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]4O[CH](CO)[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O
FormulaC16 H25 N5 O16 P2
NameGUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
ChEMBL
DrugBank
ZINCZINC000008215581
PDB chain5mm0 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5mm0 Structural basis for dolichylphosphate mannose biosynthesis.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		P8 T9 E12 D39 D89 D91 R117 V156 R202
Binding residue
(residue number reindexed from 1)		P11 T12 E15 D42 D92 D94 R120 V159 R205
Annotation score4
Enzymatic activity
Enzyme Commision number 2.4.1.83: dolichyl-phosphate beta-D-mannosyltransferase.
Gene Ontology
Molecular Function
GO:0004582 dolichyl-phosphate beta-D-mannosyltransferase activity
GO:0016757 glycosyltransferase activity
GO:0046872 metal ion binding
Biological Process
GO:0000271 polysaccharide biosynthetic process
GO:0006486 protein glycosylation
GO:0006488 dolichol-linked oligosaccharide biosynthetic process
GO:0006506 GPI anchor biosynthetic process
GO:0019348 dolichol metabolic process
GO:0035269 protein O-linked mannosylation
Cellular Component
GO:0005886 plasma membrane
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5mm0, PDBe:5mm0, PDBj:5mm0
PDBsum5mm0
PubMed28743912
UniProtQ8U4M3|DPM1_PYRFU Dolichol-phosphate mannosyltransferase (Gene Name=PF0058)

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