Structure of PDB 5kkb Chain B

Receptor sequence

>5kkbB (length=469) Species: 10090 (Mus musculus)

VDFLPPVGVENREPADATIREKRAKIKEMMTHAWNNYKRYAWGLNELKPI
SKEGHSSSLFGNIKGATIVDALDTLFIMGMKTEFQEAKSWIKKYLDFNVN
AEVSVFEVNIRFVGGLLSAYYLSGEEIFRKKAVELGVKLLPAFHTPSGIP
WALLNMKSGIGRNWPWASGGSSILAEFGTLHLEFMHLSHLSGDPVFAEKV
MKIRTVLNKLDKPEGLYPNYLNPSSGQWGQHHVSVGGLGDSFYEYLLKAW
LMSDKTDLEAKKMYFDAVQAIETHLIRKSSGGLTYIAEWKGGLLEHKMGH
LTCFAGGMFALGADGAPEARAQHYLELGAEIARTCHESYNRTYVKLGPEA
FRFDGGVEAIATRQNEKYYILRPEVIETYMYMWRLTHDPKYRTWAWEAVE
ALESHCRVNGGYSGLRDVYIARESYDDVQQSFFLAETLKYLYLIFSDDDL
LPLEHWIFNTEAHPFPILR

3D structure

• PDB: 5kkb Substrate recognition and catalysis by GH47 alpha-mannosidases involved in Asn-linked glycan maturation in the mammalian secretory pathway.
• Chain: B
• Resolution: 1.774 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): E282 R286 D415 E549
• Catalytic site (residue number reindexed from 1): E107 R111 D240 E374
• Enzyme Commision number: 3.2.1.113: mannosyl-oligosaccharide 1,2-alpha-mannosidase.

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	MAN	B	F281 E351 L413 D415	F106 E176 L238 D240
BS02	MAN	B	R547 E549 F607 E611 T635 E636	R372 E374 F432 E436 T460 E461
BS03	MAN	B	S232 S233	S57 S58
BS04	1PS	B	V312 L315 P316 H319	V137 L140 P141 H144

Gene Ontology

Molecular Function

• GO:0004571 mannosyl-oligosaccharide 1,2-alpha-mannosidase activity
• GO:0005509 calcium ion binding

Biological Process

• GO:0005975 carbohydrate metabolic process

Cellular Component

• GO:0016020 membrane

External links

• PDB: RCSB:5kkb, PDBe:5kkb, PDBj:5kkb
• PDBsum: 5kkb
• PubMed: 27856750
• UniProt: P45700|MA1A1_MOUSE Mannosyl-oligosaccharide 1,2-alpha-mannosidase IA (Gene Name=Man1a1)