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Receptor Information

>3dr7 Chain D (length=367) Species: 190650 (Caulobacter vibrioides CB15) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

PRISVAAPRLDGNERDYVLECMDTTWISSVGRFIVEFEKAFADYCGVKHA
IACNNGTTALHLALVAMGIGPGDEVIVPSLTYIASANSVTYCGATPVLVD
NDPRTFNLDAAKLEALITPRTKAIMPVHLYGQICDMDPILEVARRHNLLV
IEDAAEAVGATYRGKKSGSLGDCATFSFFGNKIITTGEGGMITTNDDDLA
AKMRLLRGQGMDPNRRYWFPIVGFNYRMTNIQAAIGLAQLERVDEHLAAR
ERVVGWYEQKLARLGNRVTKPHVALTGRHVFWMYTVRLGEGLSTTRDQVI
KDLDALGIESRPVFHPMHIMPPYAHLATDDLKIAEACGVDGLNLPTHAGL
TEADIDRVIAALDQVLV

Ligand ID

GPD

InChI

InChI=1S/C16H26N6O13P2/c1-5-6(17)2-7(23)15(32-5)34-37(29,30)35-36(27,28)31-3-8-10(24)11(25)14(33-8)22-4-19-9-12(22)20-16(18)21-13(9)26/h4-8,10-11,14-15,23-25H,2-3,17H2,1H3,(H,27,28)(H,29,30)(H3,18,20,21,26)/t5-,6+,7+,8-,10-,11-,14-,15-/m1/s1

InChIKey

DRNSMVBRYJDNAT-CYCRINRGSA-N

SMILES

Software	SMILES
CACTVS 3.341	C[C@H]1O[C@H](O[P@@](O)(=O)O[P@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4C(=O)NC(=Nc34)N)[C@@H](O)C[C@@H]1N
OpenEye OEToolkits 1.5.0	CC1C(CC(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3N=C(NC4=O)N)O)O)O)N
OpenEye OEToolkits 1.5.0	C[C@@H]1[C@H](C[C@@H]([C@H](O1)O[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3N=C(NC4=O)N)O)O)O)N
CACTVS 3.341	C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4C(=O)NC(=Nc34)N)[CH](O)C[CH]1N
ACDLabs 10.04	O=P(OC1OC(C(N)CC1O)C)(O)OP(=O)(O)OCC4OC(n2c3N=C(N)NC(=O)c3nc2)C(O)C4O

Formula

C16 H26 N6 O13 P2

Name

(2R,3S,5S,6R)-5-amino-3-hydroxy-6-methyl-oxan-2-yl

PDB chain

3dr7 Chain D Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	3dr7 Accommodation of GDP-linked sugars in the active site of GDP-perosamine synthase
Resolution	1.7 Å
Binding residue (original residue number in PDB)	A10 P12 Y86 F183 G184 N185 X186 E313 F318
Binding residue (residue number reindexed from 1)	A6 P8 Y82 F179 G180 N181 X182 E309 F314
Annotation score	3

Catalytic site (original residue number in PDB)	Y86 D157 E160 F183 K186 Y221 R231
Catalytic site (residue number reindexed from 1)	Y82 D153 E156 F179 K182 Y217 R227
Enzyme Commision number	2.6.1.102: GDP-perosamine synthase.

	Molecular Function
GO:0008483	transaminase activity
GO:0030170	pyridoxal phosphate binding
GO:0102933	GDP-4-dehydro-6-deoxy-D-mannose-4-aminotransferase activity

	Biological Process
GO:0000271	polysaccharide biosynthetic process
GO:0009103	lipopolysaccharide biosynthetic process
GO:0009243	O antigen biosynthetic process

PDB	RCSB:3dr7, PDBe:3dr7, PDBj:3dr7
PDBsum	3dr7
PubMed	18795799
UniProt	Q9A9H3\|GDPPS_CAUVC GDP-perosamine synthase (Gene Name=per)

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Structure of PDB 3dr7 Chain D Binding Site BS02