Structure of PDB 1tuf Chain B Binding Site BS01

Receptor Information
>1tuf Chain B (length=434) Species: 2190 (Methanocaldococcus jannaschii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FLGNDTVEIKDGRFFIDGYDAIELAEKFGTPLYVMSEEQIKINYNRYIEA
FKRWEEETGKEFIVAYAYKANANLAITRLLAKLGCGADVVSGGELYIAKL
SNVPSKKIVFNGNCKTKEEIIMGIEANIRAFNVDSISELILINETAKELG
ETANVAFRINPNVNPKTHPKISTGLKKNKFGLDVESGIAMKAIKMALEME
YVNVVGVHCHIGSQLTDISPFIEETRKVMDFVVELKEEGIEIEDVNLGGG
LGIPYYKDKQIPTQKDLADAIINTMLKYKDKVEMPNLILEPGRSLVATAG
YLLGKVHHIKETPVTKWVMIDAGMNDMMRPAMYEAYHHIINCKVKNEKEV
VSIAGGLCESSDVFGRDRELDKVEVGDVLAIFDVGAYGISMANNYNARGR
PRMVLTSKKGVFLIRERETYADLIAKDIVPPHLL
Ligand information
Ligand IDAZ1
InChIInChI=1S/C9H16O4/c10-8(11)6-4-2-1-3-5-7-9(12)13/h1-7H2,(H,10,11)(H,12,13)
InChIKeyBDJRBEYXGGNYIS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(CCCC(=O)O)CCCC(=O)O
ACDLabs 10.04O=C(O)CCCCCCCC(=O)O
CACTVS 3.341OC(=O)CCCCCCCC(O)=O
FormulaC9 H16 O4
NameAZELAIC ACID
ChEMBLCHEMBL1238
DrugBankDB00548
ZINCZINC000001531036
PDB chain1tuf Chain B Residue 503 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1tuf Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor
Resolution2.4 Å
Binding residue
(original residue number in PDB)		R307 R343 Y347
Binding residue
(residue number reindexed from 1)		R293 R329 Y333
Annotation score1
Binding affinityMOAD: Ki=89uM
PDBbind-CN: -logKd/Ki=4.05,Ki=89uM
Enzymatic activity
Catalytic site (original residue number in PDB) K83 H224 E304
Catalytic site (residue number reindexed from 1) K69 H210 E290
Enzyme Commision number 4.1.1.20: diaminopimelate decarboxylase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0008836 diaminopimelate decarboxylase activity
GO:0016830 carbon-carbon lyase activity
GO:0016831 carboxy-lyase activity
GO:0030170 pyridoxal phosphate binding
Biological Process
GO:0009085 lysine biosynthetic process
GO:0009089 lysine biosynthetic process via diaminopimelate

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1tuf, PDBe:1tuf, PDBj:1tuf
PDBsum1tuf
PubMed12429091
UniProtQ58497|DCDA_METJA Diaminopimelate decarboxylase (Gene Name=lysA)

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