Structure of PDB 2vr5 Chain B Binding Site BS02

Receptor Information
>2vr5 Chain B (length=714) Species: 2287 (Saccharolobus solfataricus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FRTRDRPLRPGDPYPLGSNWIEDDDGVNFSLFSENAEKVELLLYSLTNQK
YPKEIIEVKNKTGDIWHVFVPGLRPGQLYAYRVYGPYKPELGLRFNPNKV
LIDPYAKAINGSVIWNDAVFGYKIGDQNQDLTYDERDSGEYVPKSVVINP
YFEWDDEDFIKGKKVPLKDTVIYEVHVKGFTKLRLDLPENIRGTYEGLAS
EQMISYLKDLGITTVELMPVFHFIDQRFLTDKGLTNYWGYDPINFFSPEC
RYSSTGCLGGQVLSFKKMVNELHNAGIEVIIDVVYNHTAEGNHLGPTLSF
RGIDNTAYYMLQPDNKRYYLDFTGTGNTLNLSHPRVIQMVLDSLRYWVTE
MHVDGFRFDLAAALARELYSVNMLNTFFIALQQDPILSQVKLIAEPWDVG
QGGYQVGNFPYQWAEWNGKYRDSIRRFWRGEALPYSEIANRLLGSPDIYL
GNNKTPFASINYVTSHDGFTLEDLVSYNQKHNEANGFNNQDGMNENYSWN
CGAEGPTNDQNVVICREKQKRNFMITLLVSQGTPMILGGDELSRTQRGNN
NAFCQDNEITWFDWNLDERKSKFLEFVKKMIQFYRAHPAFRRERYFQGKK
LFGMPLKDVTFYTLEGREVDEKTWSSPTQLVIFVLEGSVMDEINMYGERI
ADDSFLIILNANPNNVKVKFPKGKWELVISSYLREIKPEERIIEGEKELE
IEGRTALVYRRIEL
Ligand information
Ligand IDA16
InChIInChI=1S/C19H35NO13/c1-5-9(20-7-2-6(3-21)10(23)13(26)11(7)24)12(25)16(29)19(31-5)33-17-8(4-22)32-18(30)15(28)14(17)27/h5-30H,2-4H2,1H3/t5-,6-,7+,8-,9-,10-,11+,12+,13+,14-,15-,16-,17-,18-,19-/m1/s1
InChIKeyARPGGXAVVRZVTA-FCTHMPQMSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[CH]1O[CH](O[CH]2[CH](O)[CH](O)[CH](O)O[CH]2CO)[CH](O)[CH](O)[CH]1N[CH]3C[CH](CO)[CH](O)[CH](O)[CH]3O
OpenEye OEToolkits 1.5.0C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@H]2[C@H](O[C@H]([C@@H]([C@H]2O)O)O)CO)O)O)N[C@H]3CC([C@H]([C@@H]([C@H]3O)O)O)CO
CACTVS 3.341C[C@H]1O[C@H](O[C@H]2[C@H](O)[C@@H](O)[C@H](O)O[C@@H]2CO)[C@H](O)[C@@H](O)[C@@H]1N[C@H]3C[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0CC1C(C(C(C(O1)OC2C(OC(C(C2O)O)O)CO)O)O)NC3CC(C(C(C3O)O)O)CO
ACDLabs 10.04OC3C(OC2OC(C)C(NC1CC(CO)C(O)C(O)C1O)C(O)C2O)C(OC(O)C3O)CO
FormulaC19 H35 N O13
Name4-O-(4,6-dideoxy-4-{[(1S,2S,3S,4R,5S)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}-alpha-D-glucopyranosyl)-beta-D-glucopyranose
ChEMBL
DrugBank
ZINCZINC000064511976
PDB chain2vr5 Chain B Residue 1720 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2vr5 Structural Insight Into the Bifunctional Mechanism of the Glycogen-Debranching Enzyme Trex from the Archaeon Sulfolobus Solfataricus.
Resolution2.8 Å
Binding residue
(original residue number in PDB)
W242 Y244 H291 D363 H470 D471
Binding residue
(residue number reindexed from 1)
W238 Y240 H287 D359 H466 D467
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) S116 H226 F227 E253 D363 E399 D471
Catalytic site (residue number reindexed from 1) S112 H222 F223 E249 D359 E395 D467
Enzyme Commision number 3.2.1.-
Gene Ontology
Molecular Function
GO:0004133 glycogen debranching enzyme activity
GO:0004177 aminopeptidase activity
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0005980 glycogen catabolic process

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:2vr5, PDBe:2vr5, PDBj:2vr5
PDBsum2vr5
PubMed18703518
UniProtP95868

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