Structure of PDB 5i0d Chain B

Receptor sequence

>5i0dB (length=1060) Species: 169963 (Listeria monocytogenes EGD-e)

MDGEYHSPYGDDDLYTVQPTERSPRDPKAGEDVILNITTWPIENGQDVWV
EWTKNGVAQENVTAAYDYNSGNNTYWKADLGKFEKGDEITYTTKGSTNGG
TAYESGPFTFYVTDWEYVQDVTSVVDNGDSITLNMTATAGDFSPKLYLSF
EDLDTLRMELSPTGKETGHAGKSGYTVEDTAEKVTVTTEDLSIEIQKSPY
RMEVHQADGTLLTSEYTTANSLGWLTDGKNVINQYQNNFMTPSDEAFYGF
GERYDTINQRGKDVETYVYNEYQDQAQTERTYLAVPFFVSANKYGMYVNS
DFHSQFQMASKVEDKYSFVLDNDGDMTNMLDYYVISGKDQNDIVNNYTDI
TGKTTLLPKWAFGLWMSANEWDRESDVSSALSNAKANDIPATGFVLEQWS
DEETYYIWNNATYTAKKNGEAFSYDDFTFNGKWTDPKGMVDSVHDAGMNI
VLWQVPVLKDDGTVYEQRDNDEEYMISQGYSADDGTGAPYRVPASQWFGN
GILLDFTNKDAVDWWTSQREYLLTEVGIDGFKTDGGEMVWGRDTTFSNGE
KGQEMRNRYPTDYVSSYFDFAKSINPEAVSFSRSGTSGAQKSGIYWSGDQ
TSTFDSFQASLKAGLSASTSGVSYWAWDMAGFTGDYPTAELYKRATAMAA
FAPIMQFHSEKSDPSPSEERSPWNAVARTGDETILPTFQKYLYTRMNLLP
YIYTAAKDTADNGKSMMRQMAMDYPEDVNARDLDEQYMFGDDLLVAPIVQ
EGQTEKEVYLPEGEWVDIWNGGVHPGGETISYYADVDTLPVFAKAGAIIP
MNMTDGYQLGQNVGNDLKSYDNLTFRVYPSGDSEYSFYDDVNGGEMRDIS
VSEDFANEKVSVDLPAMADETTMQVFSTEPTSVTIDGADVAKADTLDAFN
EATTGYYYDTVQNLTYVKAAAKDAKQAIVLNGVNHAPYEAEFGHLTNVTT
ASDHAGYTGTGFVAGFDAEKEAVEFDIDAVDGASDYTMEVRYSAGVEDAT
RTVYINGKKQQITLPKTANWDTWNTVEVPVTLQAGNNQVVFDFEADDTAG
INFDHVVIKK

3D structure

• PDB: 5i0d Transferase Versus Hydrolase: The Role of Conformational Flexibility in Reaction Specificity.
• Chain: B
• Resolution: 1.77 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	B	E428 D565 R614 W627 D630 F663 H689	E397 D534 R583 W596 D599 F632 H658
BS02	GLC	B	N400 Q429 E433	N369 Q398 E402
BS03	GLC	B	N301 W528 R614 D630 E691	N270 W497 R583 D599 E660
BS04	GLC	B	T443 Y444 Y496 E497 Q498	T412 Y413 Y465 E466 Q467
BS05	GLC	B	D798 N801 H805 Y813 Y814	D767 N770 H774 Y782 Y783
BS06	GLC	B	Y303 E691	Y272 E660
BS07	GLC	B	G665 K692	G634 K661
BS08	GLC	B	D78 T94	D47 T63
BS09	GLC	B	H985 W1051 N1083	H954 W1020 N1052
BS10	GLC	B	D998 V1027 A1080 G1081	D967 V996 A1049 G1050
BS11	MG	B	E401 D403 D407	E370 D372 D376
BS12	CA	B	E970 E972 T989 G992 D1085	E939 E941 T958 G961 D1054
BS13	GLC	B	Q429 E433 S693	Q398 E402 S662

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
• GO:0016798 hydrolase activity, acting on glycosyl bonds
• GO:0030246 carbohydrate binding
• GO:0046872 metal ion binding

Biological Process

• GO:0005975 carbohydrate metabolic process

External links

• PDB: RCSB:5i0d, PDBe:5i0d, PDBj:5i0d
• PDBsum: 5i0d
• PubMed: 28089449
• UniProt: Q8Y4J2