Structure of PDB 3kdn Chain I

Receptor sequence

>3kdnI (length=436) Species: 69014 (Thermococcus kodakarensis KOD1)

YDYYVDKGYEPSKKRDIIAVFRVTPAEGYTIEQAAGAVAAESSTGTWTTL
YPWYEQERWADLSAKAYDFHDMGDGSWIVRIAYPFHAFEEANLPGLLASI
AGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIKDRPIY
GVVPKPKVGYSPEEFEKLAYDLLSNGADYMKDDENLTSPWYNRFEERAEI
MAKIIDKVENETGEKKTWFANITADLLEMEQRLEVLADLGLKHAMVDVVI
TGWGALRYIRDLAADYGLAIHGHRAMHAAFTRNPYHGISMFVLAKLYRLI
GIDQLHVGTAGAGKLEGERDITIQNARILRESHYKPDENDVFHLEQKFYS
IKAAFPTSSGGLHPGNIQPVIEALGTDIVLQLGGGTLGHPDGPAAGARAV
RQAIDAIMQGIPLDEYAKTHKELARALEKWGHVTPV

3D structure

• PDB: 3kdn Structure-based catalytic optimization of a type III Rubisco from a hyperthermophile
• Chain: I
• Resolution: 2.09 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): K163 K189 D190 D191 E192 H281 H314 K322
• Catalytic site (residue number reindexed from 1): K155 K181 D182 D183 E184 H273 H306 K314
• Enzyme Commision number: 4.1.1.39: ribulose-bisphosphate carboxylase.

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	CAP	I	W55 N111	W47 N103
BS02	MG	I	K189 D191 E192	K181 D183 E184
BS03	CAP	I	K163 K189 D191 E192 H281 R282 H314 K322 L323 S367 G368 G369 Q389 G391 G392	K155 K181 D183 E184 H273 R274 H306 K314 L315 S359 G360 G361 Q381 G383 G384

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0016491 oxidoreductase activity
• GO:0016829 lyase activity
• GO:0016984 ribulose-bisphosphate carboxylase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006196 AMP catabolic process
• GO:0015977 carbon fixation

External links

• PDB: RCSB:3kdn, PDBe:3kdn, PDBj:3kdn
• PDBsum: 3kdn
• PubMed: 20926376
• UniProt: O93627|RBL_THEKO Ribulose bisphosphate carboxylase (Gene Name=rbcL)