Structure of PDB 3kdo Chain B

Receptor sequence

>3kdoB (length=438) Species: 69014 (Thermococcus kodakarensis KOD1)

TIYDYYVDKGYEPSKKRDIIAVFRVTPAEGYTIEQAAGAVAAESSTGTWT
TLYPWYEQERWADLSAKAYDFHDMGDGSWIVRIAYPFHAFEEANLPGLLA
SIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIKDRP
IYGVVPKPKVGYSPEEFEKLAYDLLSNGADYMKDDENLTSPWYNRFEERA
EIMAKIIDKVENETGEKKTWFANITADLLEMEQRLEVLADLGLKHAMVDV
VITGWGALRYIRDLAADYGLAIHGHRAMHAAFTRNPYHGISMFVLAKLYR
LIGIDQLHVGTAGAGKLEGERDITLGFVDLLRESHYKPDENDVFHLEQKF
YSIKAAFPTSSGGLHPGNIQPVIEALGTDIVLQLGGGTLGHPDGPAAGAR
AVRQAIDAIMQGIPLDEYAKTHKELARALEKWGHVTPV

3D structure

• PDB: 3kdo Structure-based catalytic optimization of a type III Rubisco from a hyperthermophile
• Chain: B
• Resolution: 2.36 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): K157 K183 D184 D185 E186 H275 H308 K316
• 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	B	K163 K189 D191 E192 H281 R282 H314 K322 L323 S367 G368 G369 G391	K157 K183 D185 E186 H275 R276 H308 K316 L317 S361 G362 G363 G385
BS02	MG	B	K189 D191 E192	K183 D185 E186
BS03	CAP	B	W55 N111	W49 N105

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