Structure of PDB 5d0f Chain B

Receptor sequence

>5d0fB (length=1526) Species: 284593 (Nakaseomyces glabratus CBS 138)

AHRTLLLRLSDSGEPVTSCSYGQGVLTLPSLPLPQGKKLGDMPVYTVKLA
IPAGSPVTRDGLIWTNCPPDFSTQFDREKFYKKIIKTSFHEDDHIDLDIY
VPGTYCFYLSFKNDKDELETTRKFYFVVLPILSVNDKFIPLNSIAMQSVV
SKWMGPTIKDWEKVFARVASKKYNMIHFTPLQHRGESNSPYSIYDQLEFD
PTVFKSEKEVADMVERLRTEHNILSLTDIVFNHTANNSQWLLDHPEAGYN
HKTSPHLISAIELDKKLLDFSEQMEALGYPVDLKTVDDLIKVMDGIKEHV
IGELKLWEFYVVDVKQTVSELREKWGNSKSWSDDNIPSKDDSTNLAQFVR
DNATEPGFGSLGERGSNKINIDKFAAILKKLHSEDYNNGIEELATKILND
INLPFYKEYDDDINEVLEQLFNRIKYLRIDDHGPKQGPITKKLPLSEPYF
TRFKAKDGEEYALANNGWIWDGNPLVDFASSQSKAYLRREVIVWGDCVKL
RYGKGPSDSPYLWERMSKYVEMNARIFNGFRIDNCHSTPLHVGQYFLDVA
RRVNPNLYVVAQLFSGSEAMDCLFVERLGISSLIREAMQAWSEEELSRLV
HRHGGRPIGSYKFVPLDDFPYPADVKIDEEYCAYNPDDHSVKCVSEIMIP
KTLTATPPHALFMDCTHDNETPNQKRTVEDTLPNAALVAFCSSAIGSVYG
YDEVFPQLLDLVQEKRTYSCAENTGISKVKTLLNNMREEIASEAVDIEDS
EMHVHHDGQYITFHRTNAKNGKGWYLVARTKFHSSGDQMLPRIKLSQTKA
TFKAAFSLERTGDAPISDEIIEGIPTKLRELTGFDIGFDENTKETSILLP
QDFPQGSIVIFETQQLGIDDSLDHFIRSGAIKATEKLSLESINYVLYRAE
QEEYDYSEGRSGAYDIPDYGKPVYCGLQGWVSILRKIIFYNDLAHPLSNN
LRNGHWAVDYVVNRLDLYKDKEGVAEVQEWLRSRMERIKQLPSYLVPSFF
ALVVGIMYGCCRLRAMQLMSDNVGKSTVFVQSLAMTSIQMVSAMKSTSIL
PDQNIAAMAAGLPHFSTNYMRCWGRDVFISLRGLLLTTGRYEEAKEHILA
FAKTLKHGLIPNLLDAGRNPRYNARDAAWFFVQAIQDYVTIVPGGVSLLQ
EKVTRRFPLDDEYIPYDDPKAFSYSSTIEEIIYEILNRHAGGIKYREANA
GPNLDRVMKDEGFNVEVNVDWETGLIHGGSQFNCGTWMDKMGESEKANSV
GVPGTPRDGAAVEINGLLKSCLRFVLQLSKDGKFKYTEVTKPDGSKISLS
SWNDLLQENFERCFYVPKNKEDDNKFEIDATIINRRGIYKDLYRSGKPYE
DYQFRPNFTIAMVVAPELFTPDYAAGAIELADQVLRGPVGMRTLDPSDYN
YRPYYNNGEDSDDFATSKGRNYHQGPEWVWCYGYFIRAYHYFNFLTNPKC
QVEGSAKKLKPSSYLYRKLYSRLLKHREWIENSPWAGLAELTNKDGEVCN
DSSPTQAWSTGCLLDLFYDLWISYEE

3D structure

• PDB: 5d0f Crystal structure of glycogen debranching enzyme and insights into its catalysis and disease-causing mutations.
• Chain: B
• Resolution: 3.3 Å

Enzymatic activity

• Enzyme Commision number: 2.4.1.25: 4-alpha-glucanotransferase.
  3.2.1.33: amylo-alpha-1,6-glucosidase.

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	B	Y193 H235 W496 D535 N536 Q564 D670	Y191 H233 W494 D533 N534 Q562 D668
BS02	GLC	B	S191 D498	S189 D496
BS03	GLC	B	D498 V714	D496 V712
BS04	GLC	B	K444 E449 G497	K442 E447 G495
BS05	GLC	B	H1066 Y1407 D1503	H1064 Y1405 D1501
BS06	GLC	B	W1075 D1241 M1243	W1073 D1239 M1241
BS07	GLC	B	L1115 R1123 L1206 D1207 R1208	L1113 R1121 L1204 D1205 R1206
BS08	GLC	B	P919 W958	P917 W956
BS09	GLC	B	Y916 D917	Y914 D915
BS10	GLC	B	S1399 Y1401	S1397 Y1399
BS11	GLC	B	Y1351 D1400 Y1401 N1402	Y1349 D1398 Y1399 N1400
BS12	GLC	B	R425 Y428	R423 Y426
BS13	GLC	B	Q421 W472	Q419 W470

Gene Ontology

Molecular Function

• GO:0004134 4-alpha-glucanotransferase activity
• GO:0004135 amylo-alpha-1,6-glucosidase activity
• GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
• GO:0016757 glycosyltransferase activity
• GO:0016798 hydrolase activity, acting on glycosyl bonds

Biological Process

• GO:0005975 carbohydrate metabolic process
• GO:0005978 glycogen biosynthetic process
• GO:0005980 glycogen catabolic process

Cellular Component

• GO:0005575 cellular_component
• GO:0005737 cytoplasm

External links

• PDB: RCSB:5d0f, PDBe:5d0f, PDBj:5d0f
• PDBsum: 5d0f
• PubMed: 27088557
• UniProt: Q6FSK0