Structure of PDB 4d1j Chain D Binding Site BS01

Receptor Information
>4d1j Chain D (length=540) Species: 498211 (Cellvibrio japonicus Ueda107) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AAPLPELLSNNGKHALMVDGAPYIILGSQTNNSSNYPDALKDVWPSMEKM
GANTLSIPVAWEQIEPVEGQFDFSFVDVLLKEARQRKVRLVLLWFATWKN
NAPHYAPAWVKLDNARFPRVVKEDGDTLNSLSPLGQNTLAADKKAFVELM
KYLAKRDKDHTVIMVQVQNEVGTYGAVRDYSPMAQAVFNAAVPDDLIQKL
QLKPGTWSQVFGRDADEFFHAYQIARYCDEVTVAGKAIKNLPMYVNVALR
NPFNPGLPGQYSSGGGTDNVLHIWKAAAPNIDLIAPDIYFRDYKTVSKVL
ELYTRPDNALFVAEIGNDQPFARYLFPTLGKGGIGFSPFGMDDTDYTNYP
LGAKVYNDETIEQFAQVYRLVNPMMREWARLSYQGQVWGVAEPLDSTTET
QKIWNAEATPEEKEQHKKDRASALTQQLDLGLWDAEVTYGRPMFWVTPPE
GNTPAAGGALIAQLDDNEYLVTAYKARVEFKPSQELAGKKFMIERVEEGR
FEKGKWVMERVWNGDQTDWGLNFTDRPHLLRVKMASYSVQ
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 chain4d1j Chain D Residue 600 [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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PDB4d1j A Complex Gene Locus Enables Xyloglucan Utilization in the Model Saprophyte Cellvibrio Japonicus.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		N67 K134 N135 N204 E205 E349 F374 N383
Binding residue
(residue number reindexed from 1)		N32 K99 N100 N169 E170 E314 F339 N348
Annotation score1
Binding affinityMOAD: Kd=485nM
Enzymatic activity
Enzyme Commision number 3.2.1.23: beta-galactosidase.
Gene Ontology
Molecular Function
GO:0004565 beta-galactosidase activity
Biological Process
GO:0005975 carbohydrate metabolic process
Cellular Component
GO:0009341 beta-galactosidase complex

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Molecular Function
View graph for
Biological Process
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Cellular Component
External links
PDB RCSB:4d1j, PDBe:4d1j, PDBj:4d1j
PDBsum4d1j
PubMed25171165
UniProtB3PBE0

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