Structure of PDB 1xkd Chain A Binding Site BS01

Receptor Information

>1xkd Chain A (length=427) Species: 272557 (Aeropyrum pernix K1)

ASPPCTTEELSPPPGGSLVEYSGGSLRVPDNPVVAFIRGDGVGPEVVESA
LKVVDAAVKKVYGGSRRIVWWELLAGHLAREKCGELLPKATLEGIRLARV
ALKGPLETPVRSLNVAIRQALDLYANIRPVRYYGQPAPHKYADRVDMVIF
RENTEDVYAGIEWPHDSPEAARIRRFLAEEFGISIREDAGIGVKPISRFA
TRRLMERALEWALRNGNTVVTIMHKGNIMKYTEGAFMRWAYEVALEKFRE
HVVTEQEVQEKYGGVRPEGKILVNDRIADNMLQQIITRPWDYQVIVAPNL
NGDYISDAASALVGGIGMAAGMNMGDGIAVAEPVHGTAPKYAGKDLINPS
AEILSASLLIGEFMGWREVKSIVEYAIRKAVQSKKVTQDLARHMPGVQPL
RTSEYTETLIAYIDEADLNEVLAGKRG

Ligand information

• Ligand ID: CA
• InChI: InChI=1S/Ca/q+2
• InChIKey: BHPQYMZQTOCNFJ-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Ca++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Ca+2]
• Formula: Ca
• Name: CALCIUM ION
• DrugBank: DB14577
• PDB chain: 1xkd Chain A Residue 1006

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1xkd Isocitrate dehydrogenase from the hyperthermophile Aeropyrum pernix: X-ray structure analysis of a ternary enzyme-substrate complex and thermal stability.
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): D311 D315
• Binding residue (residue number reindexed from 1): D303 D307
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): Y166 K233 D287 D311 D315
• Catalytic site (residue number reindexed from 1): Y158 K225 D279 D303 D307
• Enzyme Commision number: 1.1.1.42: isocitrate dehydrogenase (NADP(+)).

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0000287 magnesium ion binding
• GO:0004450 isocitrate dehydrogenase (NADP+) activity
• GO:0016491 oxidoreductase activity
• GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
• GO:0046872 metal ion binding
• GO:0051287 NAD binding

Biological Process

• GO:0006097 glyoxylate cycle
• GO:0006099 tricarboxylic acid cycle

External links

• PDB: RCSB:1xkd, PDBe:1xkd, PDBj:1xkd
• PDBsum: 1xkd
• PubMed: 15581899
• UniProt: Q9YE81