Structure of PDB 6ude Chain D Binding Site BS01

Receptor Information
>6ude Chain D (length=492) Species: 1338011 (Elizabethkingia anophelis NUHP1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EKLILALDQGTTSSRAILFNKSGEIKFVSQKSFEQIFPTPGWVEHDPNEI
WSSQISVAAEVIAKAGEVAAIGITNQRETTVVWDRHTSEPIYNAIVWQDR
RTSKYCDELKSQGHTDEIKQKTGLVLDAYFSATKLKWILDNVEGAREKAE
AGDLCFGTVDTWLIWKLTRGKMFITDVSNASRTMMFNIRTMDWDDDLLKL
FNIPRAILPEVKQSSEVYGETSTTLFSTKIPIAGIAGDQQAALFGQMCTK
PGMVKNTYGTGCFLLMNTGNEAVYSKNNLLTTVAWKINGEVSYALEGSVF
VGGAAIQWLRDGLKIIHDSSEVSTLAETVEDNGGVYFVPALTGLGAPYWD
QYARGTIIGVTRGTTDGHIARATLEGIAFQVYDIVKAMEADAETQSTELR
VDGGASASNLLMQIQSDLFGFKIIRPKTLETTALGAAYLAGLAVGFWESI
DEIQSQWIIEKEFTPKEDKTKIDNMVSFWHKAVKRSQAWIED
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain6ude Chain D Residue 600 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6ude Crystal structure of Glycerol kinase from Elizabethkingia anophelis NUHP1 in complex with ADP and glycerol
Resolution1.95 Å
Binding residue
(original residue number in PDB)		R18 G266 T267 G310 I313 S327 G411 A412
Binding residue
(residue number reindexed from 1)		R15 G259 T260 G303 I306 S320 G404 A405
Annotation score5
Enzymatic activity
Enzyme Commision number 2.7.1.30: glycerol kinase.
Gene Ontology
Molecular Function
GO:0004370 glycerol kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016773 phosphotransferase activity, alcohol group as acceptor
GO:0046872 metal ion binding
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0006071 glycerol metabolic process
GO:0006072 glycerol-3-phosphate metabolic process
GO:0016310 phosphorylation
GO:0019563 glycerol catabolic process
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6ude, PDBe:6ude, PDBj:6ude
PDBsum6ude
PubMed
UniProtA0A077EJ65

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