Structure of PDB 5k2m Chain I Binding Site BS02

Receptor Information
>5k2m Chain I (length=273) Species: 69014 (Thermococcus kodakarensis KOD1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRIGITYTVLRREEMAIKERAGEFGEVVMLHEDDLLFPGNYDLDVVIIRN
VSHFKALYTARLFESEGIPTVNSSRLIFEAGDKLFATLRLAGKVPVPEWK
AALSEGGALRVPDSLGYPLVSKPVFGSWGRLLAKVNDRDSLEAVLEHRKW
MKNPLYGIHYFQEFVEKPGRDIRSYVIGGEFVGAIYRYSNHWITNTARGG
KAEPCSDPEVEELSVKAWEAFGEGALAIDIFESEKGLLVNEVNPNMEFKN
AARVTGADMAGKLVEYAVEVAKT
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 chain5k2m Chain I Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5k2m Lysine Biosynthesis of Thermococcus kodakarensis with the Capacity to Function as an Ornithine Biosynthetic System.
Resolution2.18 Å
Binding residue
(original residue number in PDB)		K83 V120 K122 S127 L132 Q162 V165 K167 D171 W192 I193 T194 N195 F231 N240 E241
Binding residue
(residue number reindexed from 1)		K83 V120 K122 S127 L132 Q162 V165 K167 D171 W192 I193 T194 N195 F231 N240 E241
Annotation score5
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0005524 ATP binding
GO:0043774 coenzyme F420-2 alpha-glutamyl ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0009085 lysine biosynthetic process
GO:0036211 protein modification process
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5k2m, PDBe:5k2m, PDBj:5k2m
PDBsum5k2m
PubMed27566549
UniProtQ5JFW0

[Back to BioLiP]