Structure of PDB 3kbm Chain A

Receptor sequence

>3kbmA (length=388) Species: 1929 (Streptomyces rubiginosus)

MNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHG
VTFHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFK
DGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKD
VRDALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHAL
AFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQN
GIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVW
ASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQAL
LDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARG

3D structure

• PDB: 3kbm Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study.
• Chain: A
• Resolution: 2.0 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): H54 D57 M88 E181 K183 E217 H220 D245 D255 D257 D287
• 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	CD	A	E217 H220 D255 D257	E217 H220 D255 D257
BS02	CD	A	E181 E217 D245 D287	E181 E217 D245 D287
BS03	GLC	A	H54 T90 W137 E181 D287	H54 T90 W137 E181 D287

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:3kbm, PDBe:3kbm, PDBj:3kbm
• PDBsum: 3kbm
• PubMed: 20541506
• UniProt: P24300|XYLA_STRRU Xylose isomerase (Gene Name=xylA)