Structure of PDB 1dah Chain A Binding Site BS02

Receptor Information
>1dah Chain A (length=224) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKRYFVTGTDTEVGKTVASCALLQAAKAAGYRTAGYKPVASGSEKTPEGL
RNSDALALQRNSSLQLDYATVNPYTFAEPTSPHIISAQEGRPIESLVMSA
GLRALEQQADWVLVEGAGGWFTPLSDTFTFADWVTQEQLPVILVVGVKLG
CINHAMLTAQVIQHAGLTLAGWVANDVTPPGKRHAEYMTTLTRMIPAPLL
GEIPWLAENPENAATGKYINLALL
Ligand information
Ligand IDDNN
InChIInChI=1S/C9H20N2O2/c1-7(10)8(11)5-3-2-4-6-9(12)13/h7-8H,2-6,10-11H2,1H3,(H,12,13)/t7-,8+/m0/s1
InChIKeyKCEGBPIYGIWCDH-JGVFFNPUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C(CCCCCC(=O)O)N)N
CACTVS 3.341C[CH](N)[CH](N)CCCCCC(O)=O
ACDLabs 10.04O=C(O)CCCCCC(N)C(N)C
OpenEye OEToolkits 1.5.0C[C@@H]([C@@H](CCCCCC(=O)O)N)N
CACTVS 3.341C[C@H](N)[C@H](N)CCCCCC(O)=O
FormulaC9 H20 N2 O2
Name7,8-DIAMINO-NONANOIC ACID
ChEMBL
DrugBankDB01715
ZINCZINC000019364244
PDB chain1dah Chain A Residue 225 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1dah Mechanism of an ATP-dependent carboxylase, dethiobiotin synthetase, based on crystallographic studies of complexes with substrates and a reaction intermediate.
Resolution1.64 Å
Binding residue
(original residue number in PDB)		S41 P79
Binding residue
(residue number reindexed from 1)		S41 P79
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) T11 E12 K15 T16 K37 S41 D54 E115
Catalytic site (residue number reindexed from 1) T11 E12 K15 T16 K37 S41 D54 E115
Enzyme Commision number 6.3.3.3: dethiobiotin synthase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004141 dethiobiotin synthase activity
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
Biological Process
GO:0009102 biotin biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1dah, PDBe:1dah, PDBj:1dah
PDBsum1dah
PubMed7669756
UniProtP13000|BIOD1_ECOLI ATP-dependent dethiobiotin synthetase BioD 1 (Gene Name=bioD1)

[Back to BioLiP]