Structure of PDB 1twi Chain D Binding Site BS02

Receptor Information
>1twi Chain D (length=434) Species: 2190 (Methanocaldococcus jannaschii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLGNDTVEIKDGRFFIDGYDAIELAEKFGTPLYVMSEEQIKINYNRYIEA
FKRWEEETGKEFIVAYAYKANANLAITRLLAKLGCGADVVSGGELYIAKL
SNVPSKKIVFNGNCKTKEEIIMGIEANIRAFNVDSISELILINETAKELG
ETANVAFRINPNVNPKTHPKISTGLKKNKFGLDVESGIAMKAIKMALEME
YVNVVGVHCHIGSQLTDISPFIEETRKVMDFVVELKEEGIEIEDVNLGGG
LGIPYYKDKQIPTQKDLADAIINTMLKYKDKVEMPNLILEPGRSLVATAG
YLLGKVHHIKETPVTKWVMIDAGMNDMMRPAMYEAYHHIINCKVKNEKEV
VSIAGGLCESSDVFGRDRELDKVEVGDVLAIFDVGAYGISMANNYNARGR
PRMVLTSKKGVFLIRERETYADLIAKDIVPPHLL
Ligand information
Ligand IDLYS
InChIInChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/p+1/t5-/m0/s1
InChIKeyKDXKERNSBIXSRK-YFKPBYRVSA-O
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCCC[NH3+])C(O)=O
ACDLabs 10.04O=C(O)C(N)CCCC[NH3+]
OpenEye OEToolkits 1.5.0C(CC[NH3+])C[C@@H](C(=O)O)N
CACTVS 3.341N[C@@H](CCCC[NH3+])C(O)=O
OpenEye OEToolkits 1.5.0C(CC[NH3+])CC(C(=O)O)N
FormulaC6 H15 N2 O2
NameLYSINE
ChEMBL
DrugBank
ZINC
PDB chain1twi Chain D Residue 1605 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1twi Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor
Resolution2.0 Å
Binding residue
(original residue number in PDB)		R307 R343 Y347 Y401
Binding residue
(residue number reindexed from 1)		R293 R329 Y333 Y387
Annotation score5
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:1twi, PDBe:1twi, PDBj:1twi
PDBsum1twi
PubMed12429091
UniProtQ58497|DCDA_METJA Diaminopimelate decarboxylase (Gene Name=lysA)

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