Structure of PDB 1ud8 Chain A Binding Site BS02

Receptor Information

>1ud8 Chain A (length=480) Species: 129736 (Bacillus sp. KSM-K38)

DGLNGTMMQYYEWHLENDGQHWNRLHDDAAALSDAGITAIWIPPAYKGNS
QADVGYGAYDLYDLGEFNQKGTVRTKYGTKAQLERAIGSLKSNDINVYGD
VVMNHKMGADFTEAVQAVQVNPTNRWQDISGAYTIDAWTGFDFSGRNNAY
SDFKWRWFHFNGVDWDQRYQENHIFRFANTNWNWRVDEENGNYDYLLGSN
IDFSHPEVQDELKDWGSWFTDELDLDGYRLDAIKHIPFWYTSDWVRHQRN
EADQDLFVVGEYWKDDVGALEFYLDEMNWEMSLFDVPLNYNFYRASQQGG
SYDMRNILRGSLVEAHPMHAVTFVDNHDTQPGESLESWVADWFKPLAYAT
ILTREGGYPNVFYGDYYGIPNDNISAKKDMIDELLDARQNYAYGTQHDYF
DHWDVVGWTREGSSSRPNSGLATIMSNGPGGSKWMYVGRQNAGQTWTDLT
GNNGASVTINGDGWGEFFTNGGSVSVYVNQ

Ligand information

• Ligand ID: NA
• InChI: InChI=1S/Na/q+1
• InChIKey: FKNQFGJONOIPTF-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  CACTVS 3.341
  OpenEye OEToolkits 1.5.0: [Na+]
• Formula: Na
• Name: SODIUM ION
• DrugBank: DB14516
• PDB chain: 1ud8 Chain A Residue 1002

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1ud8 Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38) and its sodium ion binding sites
• Resolution: 2.88 Å
• Binding residue (original residue number in PDB): G300 S301 Y302 D303 W403 D404 N427
• Binding residue (residue number reindexed from 1): G300 S301 Y302 D303 W403 D404 N427
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): D231 E261 D328
• Catalytic site (residue number reindexed from 1): D231 E261 D328
• Enzyme Commision number: 3.2.1.1: alpha-amylase.

Gene Ontology

Molecular Function

• GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
• GO:0005509 calcium ion binding
• GO:0046872 metal ion binding

Biological Process

• GO:0005975 carbohydrate metabolic process

External links

• PDB: RCSB:1ud8, PDBe:1ud8, PDBj:1ud8
• PDBsum: 1ud8
• PubMed: 12719434
• UniProt: Q93I48