Structure of PDB 6jwi Chain A

Receptor sequence

>6jwiA (length=459) Species: 559292 (Saccharomyces cerevisiae S288C)

IKELAVDEELEKEDGLIPRQKSKLCKHGDRGMCEYCSPLPPWDKEYHEKN
KIKHISFHSYLKKLNENANSYISPLSEPDFRINKRCHNGHEPWPRGICSK
CQPSAITLQQQEFRMVDHVEFQKSEIINEFIQAWRYTGMQRFGYMYGSYS
KYDNTPLGIKAVVEAIYEPPQHDEQDGLTMDVEQVKNEMLQIDRQAQEMG
LSRIGLIFTDLSDAGAGDGSVFCKRHKDSFFLSSLEVIMAARHQTRHPNV
SKYSEQGFFSSKFVTCVISGNLEGEIDISSYQVSTEAEALVTADMISGST
FPSMAYINDTTDERYVPEIFYMKSNITVKENAKPAFPVDYLLVTLTHGFP
NTDTETNSKFVSSTGFPWSNRQAMGQSQDYQELKKYLFNVASSGDFNLLH
EKISNFHLLLYINSLQILSPDEWKLLIESAVKNEWEESLLKLVSSAGWQT
LVMILQESG

3D structure

• PDB: 6jwi Structural insights into ubiquitin recognition and Ufd1 interaction of Npl4.
• Chain: A
• Resolution: 2.55 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	GLC	A	V118 E121 S268	V6 E9 S150
BS02	GLC	A	L296 T297 M298 D299 L353 M357	L178 T179 M180 D181 L235 M239
BS03	GLC	A	D294 G295 L296 F326 L353 E354	D176 G177 L178 F208 L235 E236
BS04	GLC	A	S242 E243	S124 E125
BS05	GLC	A	F470 N472	F349 N351
BS06	GLC	A	N272 F470 N472	N154 F349 N351
BS07	GLC	A	Q250 Y254	Q132 Y136
BS08	GLC	A	N246 Q250	N128 Q132
BS09	GLC	A	D126 L128	D14 L16
BS10	ZN	A	C137 H139 C145 C148	C25 H27 C33 C36
BS11	ZN	A	C204 H208 C216 C219	C86 H90 C98 C101

Gene Ontology

Biological Process

• GO:0006511 ubiquitin-dependent protein catabolic process

External links

• PDB: RCSB:6jwi, PDBe:6jwi, PDBj:6jwi
• PDBsum: 6jwi
• PubMed: 31836717
• UniProt: P33755|NPL4_YEAST Nuclear protein localization protein 4 (Gene Name=NPL4)