Structure of PDB 5vnm Chain B

Receptor sequence

>5vnmB (length=731) Species: 9606 (Homo sapiens)

EGLRVVNLLQERNMLPSTPLKPPVPNLHEDIQKLNCNPELFRCTLTSIPQ
TQALLNKAKLPLGLLLHPFKDLVQLPVVTSSTIVRCRSCRTYINPFVSFL
DQRRWKCNLCYRVNDVPEEFLEPHRRPEVQNATIEFMAPSEYMLRPPQPP
VYLFVFDVSHNAVETGYLNSVCQSLLDNLDLLPGNTRTKIGFITFDSTIH
FYGLQESLSQPQMLIVSDIEDVFIPMPENLLVNLNESKELVQDLLKTLPQ
MFTKTLETQSALGPALQAAFKLMSPTGGRMSVFQTQLPTLGVGALKPREE
PNHRSSAKMTPSTDFYKKLALDCSGQQVAVDLFLLSGQYSDLASLGCISR
YSAGSVYYYPSYHHQHNPVQVQKLQKELQRYLTRKIGFEAVMRIRCTKGL
SIHTFHGNFFVRSTDLLSLPNVNPDAGYAVQMSVEESLTDTQLVSFQSAL
LYTSSKGERRIRVHTLCLPVVSTLNDVFLGADVQAISGLLANMAVDRSMT
ASLSDARDALVNAVIDSLSAYRSSVPGLMVPFSLRLFPLFVLALLKQKSF
QTGTNARLDERIFAMCQVKNQPLVYLMLTTHPSLYRVDNLSDEGALNISD
RTIPQPPILQLSVEKLSRDGAFLMDAGSVLMLWVGKNCTQNFLSQVLGVQ
NYASIPQPMTDLPELDTPESARIIAFISWLREQRPFFPILYVIADESPMK
ANFLQNMIEDRTESALSYYEFLLHIQQQVNK

3D structure

• PDB: 5vnm ER retention is imposed by COPII protein sorting and attenuated by 4-phenylbutyrate.
• Chain: B
• Resolution: 2.765 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	ZN	B	C431 C452 C455	C86 C107 C110
BS02	CLT	B	Y437 R750 A806 L808 I818	Y92 R393 A449 L451 I461

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