Structure of PDB 1rpn Chain B Binding Site BS02

Receptor Information
>1rpn Chain B (length=321) Species: 287 (Pseudomonas aeruginosa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RSALVTGITGQDGAYLAKLLLEKGYRVHGLVARRSSDTRWRLRELGIEGD
IQYEDGDMADACSVQRAVIKAQPQEVYNLAAQSFVGASWNQPVTTGVVDG
LGVTHLLEAIRQFSPETRFYQASTSEMFGLIQAERQDENTPFYPRSPYGV
AKLYGHWITVNYRESFGLHASSGILFNHESPLRGIEFVTRKVTDAVARIK
LGKQQELRLGNVDAKRDWGFAGDYVEAMWLMLQQDKADDYVVATGVTTTV
RDMCQIAFEHVGLDYRDFLKIDPAFFRPAEVDVLLGNPAKAQRVLGWKPR
TSLDELIRMMVEADLRRVSRE
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 chain1rpn Chain B Residue 1602 [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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PDB1rpn Crystal structure of a tetrameric GDP-D-mannose 4,6-dehydratase from a bacterial GDP-D-rhamnose biosynthetic pathway.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		F86 E128 N179 E188 F189 V190 K193 L211 G212 N213 R218 F277 R279 E282
Binding residue
(residue number reindexed from 1)		F84 E126 N177 E186 F187 V188 K191 L209 G210 N211 R216 F275 R277 E280
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) T126 S127 E128 Y150 K154
Catalytic site (residue number reindexed from 1) T124 S125 E126 Y148 K152
Enzyme Commision number 4.2.1.47: GDP-mannose 4,6-dehydratase.
Gene Ontology
Molecular Function
GO:0008446 GDP-mannose 4,6-dehydratase activity
GO:0016829 lyase activity
GO:0070401 NADP+ binding
Biological Process
GO:0009103 lipopolysaccharide biosynthetic process
GO:0009243 O antigen biosynthetic process
GO:0019306 GDP-D-rhamnose biosynthetic process
GO:0019673 GDP-mannose metabolic process
GO:0042351 'de novo' GDP-L-fucose biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1rpn, PDBe:1rpn, PDBj:1rpn
PDBsum1rpn
PubMed14739333
UniProtQ51366|GM4D_PSEAE GDP-mannose 4,6-dehydratase (Gene Name=gmd)

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