Structure of PDB 6u1k Chain D Binding Site BS01

Receptor Information
>6u1k Chain D (length=320) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKAL
TALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGK
PYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKEPPVVPFDPPFF
VKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVG
VLGNVFGEASPVGEVRYEAPFYDYETKYTPGRAELLIPAPLDPGTQETVQ
ELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEA
GGVAYPELLRRLVELALTHH
Ligand information
Ligand IDDAL
InChIInChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m1/s1
InChIKeyQNAYBMKLOCPYGJ-UWTATZPHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C(=O)O)N
CACTVS 3.341C[CH](N)C(O)=O
CACTVS 3.341C[C@@H](N)C(O)=O
ACDLabs 10.04O=C(O)C(N)C
OpenEye OEToolkits 1.5.0C[C@H](C(=O)O)N
FormulaC3 H7 N O2
NameD-ALANINE
ChEMBLCHEMBL66693
DrugBankDB01786
ZINCZINC000004658556
PDB chain6u1k Chain D Residue 401 [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]
PDB6u1k d-Alanine-d-alanine ligase as a model for the activation of ATP-grasp enzymes by monovalent cations.
Resolution1.67 Å
Binding residue
(original residue number in PDB)		E13 H82 Y229 R268 G288
Binding residue
(residue number reindexed from 1)		E13 H82 Y228 R267 G287
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) V16 L19 H82 E226 R268 G288 T292
Catalytic site (residue number reindexed from 1) V16 L19 H82 E225 R267 G287 T291
Enzyme Commision number 6.3.2.4: D-alanine--D-alanine ligase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0005524 ATP binding
GO:0008716 D-alanine-D-alanine ligase activity
GO:0016874 ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
GO:0071555 cell wall organization
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:6u1k, PDBe:6u1k, PDBj:6u1k
PDBsum6u1k
PubMed32335509
UniProtQ5SHZ3|DDL_THET8 D-alanine--D-alanine ligase (Gene Name=ddl)

[Back to BioLiP]