Structure of PDB 4fns Chain D Binding Site BS01

Receptor Information
>4fns Chain D (length=718) Species: 1422 (Geobacillus stearothermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KQFHLRAGKASYVMQLFRSGYLAHVYWGKAVRDVRGARAFPRLDRAFSPN
PDPSDRTFSLDTLLQEYPAYGNTDFRAPAYQVQLENGSTVTDLRYKTHRI
YKGKPRLNGLPATYVEHEQEAETLEIVLGDALIGLEVTLQYTAYEKWNVI
TRSARFENKGGERLKLLRALSMSVDFPTADYDWIHLPGAWGRERWIERRP
LVTGVQAAESRRGASSHQQNPFIALVAKNADEHQGEVYGFSFVYSGNFLA
QIEVDQFGTARVSMGINPFDFTWLLQPGESFQTPEVVMVYSDQGLNGMSQ
TYHELYRTRLARGAFRDRERPILINNWEATYFDFNEEKIVNIARTEAELG
IELVVLDDGWFGERDDDRRSLGDWIVNRRKLPNGLDGLAKQVNELGLQFG
LWVEPEMVSPNSELYRKHPDWCLHVPNRPRSEGRNQLVLDYSREDVCDYI
IETISNVLASAPITYVKWDMNRHMTEIGSSALPPERQRETAHRYMLGLYR
VMDEITSRLPHILFESCSGGGGRFDPGMLYYMPQTWTSDNTDAVSRLKIQ
YGTSLVYPISAMGAHVSAVPNHQVGRVASLKTRGHVAMSGNFGYELDITK
LTETEKQMMKQQVAFYKDVRRLVQFGTFYRLLSPFEGNEAAWMFVSADRS
EALVAYFRVLAEANAPLSYLRLKGLDSNQDYEIEGLGVYGGDELVYAGVA
LPYRSSDFISMMWRLKAV
Ligand information
Ligand IDDGJ
InChIInChI=1S/C6H13NO4/c8-2-3-5(10)6(11)4(9)1-7-3/h3-11H,1-2H2/t3-,4+,5+,6-/m1/s1
InChIKeyLXBIFEVIBLOUGU-DPYQTVNSSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01OC1C(NCC(O)C1O)CO
OpenEye OEToolkits 1.7.2C1C(C(C(C(N1)CO)O)O)O
OpenEye OEToolkits 1.7.2C1[C@@H]([C@H]([C@H]([C@H](N1)CO)O)O)O
CACTVS 3.370OC[CH]1NC[CH](O)[CH](O)[CH]1O
CACTVS 3.370OC[C@H]1NC[C@H](O)[C@@H](O)[C@H]1O
FormulaC6 H13 N O4
Name(2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol;
1-deoxygalactonojirimycin
ChEMBLCHEMBL110458
DrugBankDB05018
ZINCZINC000001636704
PDB chain4fns Chain D Residue 801 [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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PDB4fns The molecular mechanism of the thermostable alpha-galactosidases AgaA and AgaB explained by X-ray crystallography and mutational studies
Resolution2.6 Å
Binding residue
(original residue number in PDB)		W336 D366 D367 W411 R443 K476 D478 N480 C526 G528 D548
Binding residue
(residue number reindexed from 1)		W327 D357 D358 W402 R434 K467 D469 N471 C517 G519 D539
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.70,Ki=0.2uM
Enzymatic activity
Enzyme Commision number 3.2.1.22: alpha-galactosidase.
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0004557 alpha-galactosidase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0016052 carbohydrate catabolic process
GO:0033531 stachyose metabolic process
GO:0034484 raffinose catabolic process
GO:0051289 protein homotetramerization

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4fns, PDBe:4fns, PDBj:4fns
PDBsum4fns
PubMed23012371
UniProtQ9ALJ4|AGAA_GEOSE Alpha-galactosidase AgaA (Gene Name=agaA)

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