Structure of PDB 6irk Chain A

Receptor sequence

>6irkA (length=386) Species: 1929 (Streptomyces rubiginosus)

YQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVT
FHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDG
GFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVR
DALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAF
IERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQNGI
KYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWAS
AAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLD
DRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARG

3D structure

• PDB: 6irk Nylon mesh-based sample holder for fixed-target serial femtosecond crystallography.
• Chain: A
• Resolution: 1.75 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H54 D57 M88 E181 K183 E217 H220 D245 D255 D257 D287
• Catalytic site (residue number reindexed from 1): H52 D55 M86 E179 K181 E215 H218 D243 D253 D255 D285
• Enzyme Commision number: 5.3.1.5: xylose isomerase.

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	MG	A	E181 E217 D245 D287	E179 E215 D243 D285
BS02	MG	A	E217 H220 D255 D257	E215 H218 D253 D255

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0009045 xylose isomerase activity
• GO:0016853 isomerase activity
• GO:0042802 identical protein binding
• GO:0046872 metal ion binding

Biological Process

• GO:0005975 carbohydrate metabolic process
• GO:0042732 D-xylose metabolic process

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:6irk, PDBe:6irk, PDBj:6irk
• PDBsum: 6irk
• PubMed: 31061502
• UniProt: P24300|XYLA_STRRU Xylose isomerase (Gene Name=xylA)