Structure of PDB 7yk5 Chain B

Receptor sequence

>7yk5B (length=481) Species: 2850 (Phaeodactylum tricornutum)

SVSERTRIKSDRYESGVIPYAKMGYWDAAYAVKNTDVLALFRITPQPGVD
PVEAAAAVAGESSTATWTVVWTDLLTACDRYRAKAYRVDPVPNTTDQYFA
FIAYECDLFEEGSLANLTASIIGNVFGFKAVSALRLEDMRIPHSYLKTFQ
GPATGVIVERERLNKYGIPLLGATVKPKLGLSGKNYGRVVYEGLKGGLDF
LKDDENINSQPFMRWRERFLYCMEGINRASAATGETKGSYLNITAGTMEE
VYKRAEYAKTVGSIVVMIDLVMGYTAIQSAAIWARDNDLILHLHRAGNST
YARQKNHGINFRVICKWMRMCGVDHIHAGTVVGKLEGDPLMIKGFYDTLL
LTHLNVNLPYGIFFEMTWASLRKCMPVASGGIHCGQMHQLVHYLGDDVVL
QFGGGTIGHPDGIQAGATANRVALEAMILARNEGADYFNSDIGPQILRNA
AKTCGPLQTALDLWKDISFNYTSTDTSDFSV

3D structure

• PDB: 7yk5 A linker protein from a red-type pyrenoid phase separates with Rubisco via oligomerizing sticker motifs.
• Chain: B
• Resolution: 2.0 Å

Enzymatic activity

• 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	peptide	B	V35 N37 Y89 R90 D92 F104	V32 N34 Y86 R87 D89 F101
BS02	CAP	B	T69 N127	T66 N124
BS03	CAP	B	K179 E208 R298 H330 K337 S382 G383 G406	K176 E205 R295 H327 K334 S379 G380 G403

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0004497 monooxygenase activity
• GO:0016829 lyase activity
• GO:0016984 ribulose-bisphosphate carboxylase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0015977 carbon fixation
• GO:0015979 photosynthesis
• GO:0019253 reductive pentose-phosphate cycle

Cellular Component

• GO:0009507 chloroplast

External links

• PDB: RCSB:7yk5, PDBe:7yk5, PDBj:7yk5
• PDBsum: 7yk5
• PubMed: 37311001
• UniProt: Q9TK52|RBL_PHATC Ribulose bisphosphate carboxylase large chain (Gene Name=rbcL)