Structure of PDB 5k2m Chain I

Receptor sequence

>5k2mI (length=273) Species: 69014 (Thermococcus kodakarensis KOD1)

MRIGITYTVLRREEMAIKERAGEFGEVVMLHEDDLLFPGNYDLDVVIIRN
VSHFKALYTARLFESEGIPTVNSSRLIFEAGDKLFATLRLAGKVPVPEWK
AALSEGGALRVPDSLGYPLVSKPVFGSWGRLLAKVNDRDSLEAVLEHRKW
MKNPLYGIHYFQEFVEKPGRDIRSYVIGGEFVGAIYRYSNHWITNTARGG
KAEPCSDPEVEELSVKAWEAFGEGALAIDIFESEKGLLVNEVNPNMEFKN
AARVTGADMAGKLVEYAVEVAKT

3D structure

• PDB: 5k2m Lysine Biosynthesis of Thermococcus kodakarensis with the Capacity to Function as an Ornithine Biosynthetic System.
• Chain: I
• Resolution: 2.18 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	peptide	I	V51 S52 H53 F54 F125 W128 R130 N153 Y156 N245	V51 S52 H53 F54 F125 W128 R130 N153 Y156 N245
BS02	ADP	I	K83 V120 K122 S127 L132 Q162 V165 K167 D171 W192 I193 T194 N195 F231 N240 E241	K83 V120 K122 S127 L132 Q162 V165 K167 D171 W192 I193 T194 N195 F231 N240 E241
BS03	UN1	I	R173 N195 T196 A197 E247 F248 N250	R173 N195 T196 A197 E247 F248 N250

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

External links

• PDB: RCSB:5k2m, PDBe:5k2m, PDBj:5k2m
• PDBsum: 5k2m
• PubMed: 27566549
• UniProt: Q5JFW0