Structure of PDB 5vnf Chain B

Receptor sequence

>5vnfB (length=729) Species: 9606 (Homo sapiens)

EGLRVVNLLQERNMLPSTPLKPPVPNLHEDIQKLNCNPELFRCTLTSIPQ
TQALLNKAKLPLGLLLHPFKDLVQLPVVTSSTIVRCRSCRTYINPFVSFL
DQRRWKCNLCYRVNDVPEEEPHRRPEVQNATIEFMAPSEYMLRPPQPPVY
LFVFDVSHNAVETGYLNSVCQSLLDNLDLLPGNTRTKIGFITFDSTIHFY
GLQESLSQPQMLIVSDIEDVFIPMPENLLVNLNESKELVQDLLKTLPQMF
TKTLETQSALGPALQAAFKLMSPTGGRMSVFQTQLPTLGVGALKPREEPN
HRSSAKMTPSTDFYKKLALDCSGQQVAVDLFLLSGQYSDLASLGCISRYS
AGSVYYYPSYHHQHNPVQVQKLQKELQRYLTRKIGFEAVMRIRCTKGLSI
HTFHGNFFVRSTDLLSLPNVNPDAGYAVQMSVEESLTDTQLVSFQSALLY
TSSKGERRIRVHTLCLPVVSTLNDVFLGADVQAISGLLANMAVDRSMTAS
LSDARDALVNAVIDSLSAYRSSVPGLMVPFSLRLFPLFVLALLKQKSFQT
GTNARLDERIFAMCQVKNQPLVYLMLTTHPSLYRVDNLSDEGALNISDRT
IPQPPILQLSVEKLSRDGAFLMDAGSVLMLWVGKNCTQNFLSQVLGVQNY
ASIPQPMTDLPELDTPESARIIAFISWLREQRPFFPILYVIADESPMKAN
FLQNMIEDRTESALSYYEFLLHIQQQVNK

3D structure

• PDB: 5vnf ER retention is imposed by COPII protein sorting and attenuated by 4-phenylbutyrate.
• Chain: B
• Resolution: 2.407 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	B	R430 Y437 Y496 V748 R750 R752 L773	R85 Y92 Y140 V389 R391 R393 L414
BS02	ZN	B	C431 C452 C455	C86 C107 C110

Gene Ontology

Molecular Function

• GO:0008270 zinc ion binding

Biological Process

• GO:0006886 intracellular protein transport
• GO:0006888 endoplasmic reticulum to Golgi vesicle-mediated transport

Cellular Component

• GO:0030127 COPII vesicle coat

External links

• PDB: RCSB:5vnf, PDBe:5vnf, PDBj:5vnf
• PDBsum: 5vnf
• PubMed: 28594326
• UniProt: O95486|SC24A_HUMAN Protein transport protein Sec24A (Gene Name=SEC24A)