Structure of PDB 5vni Chain B

Receptor sequence

>5vniB (length=727) Species: 9606 (Homo sapiens)

LRVVNLLQERNMLPSTPLKPPVPNLHEDIQKLNCNPELFRCTLTSIPQTQ
ALLNKAKLPLGLLLHPFKDLVQLPVVTSSTIVRCRSCRTYINPFVSFLDQ
RRWKCNLCYRVNDVPEEEPHRRPEVQNATIEFMAPSEYMLRPPQPPVYLF
VFDVSHNAVETGYLNSVCQSLLDNLDLLPGNTRTKIGFITFDSTIHFYGL
QESLSQPQMLIVSDIEDVFIPMPENLLVNLNESKELVQDLLKTLPQMFTK
TLETQSALGPALQAAFKLMSPTGGRMSVFQTQLPTLGVGALKPREEPNHR
SSAKMTPSTDFYKKLALDCSGQQVAVDLFLLSGQYSDLASLGCISRYSAG
SVYYYPSYHHQHNPVQVQKLQKELQRYLTRKIGFEAVMRIRCTKGLSIHT
FHGNFFVRSTDLLSLPNVNPDAGYAVQMSVEESLTDTQLVSFQSALLYTS
SKGERRIRVHTLCLPVVSTLNDVFLGADVQAISGLLANMAVDRSMTASLS
DARDALVNAVIDSLSAYRSSVPGLMVPFSLRLFPLFVLALLKQKSFQTGT
NARLDERIFAMCQVKNQPLVYLMLTTHPSLYRVDNLSDEGALNISDRTIP
QPPILQLSVEKLSRDGAFLMDAGSVLMLWVGKNCTQNFLSQVLGVQNYAS
IPQPMTDLPELDTPESARIIAFISWLREQRPFFPILYVIADESPMKANFL
QNMIEDRTESALSYYEFLLHIQQQVNK

3D structure

• PDB: 5vni ER retention is imposed by COPII protein sorting and attenuated by 4-phenylbutyrate.
• Chain: B
• Resolution: 2.788 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 R435 Y496 R750 R752	R83 R88 Y138 R389 R391
BS02	ZN	B	C431 C452 C455	C84 C105 C108

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