Structure of PDB 3kbv Chain A Binding Site BS01

Receptor Information

>3kbv Chain A (length=388) Species: 1929 (Streptomyces rubiginosus)

MNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHG
VTFHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFK
DGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKD
VRDALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHAL
AFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQN
GIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVW
ASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQAL
LDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARG

Ligand information

• Ligand ID: NI
• InChI: InChI=1S/Ni/q+2
• InChIKey: VEQPNABPJHWNSG-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Ni++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Ni+2]
• Formula: Ni
• Name: NICKEL (II) ION
• DrugBank: DB14204
• PDB chain: 3kbv Chain A Residue 391

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3kbv Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): E217 H220 D255 D257
• Binding residue (residue number reindexed from 1): E217 H220 D255 D257
• Annotation score: 1

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.

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