Structure of PDB 6u1d Chain A

Receptor sequence

>6u1dA (length=324) Species: 300852 (Thermus thermophilus HB8)

MEMRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEK
ALTALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELL
GKPYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDP
PFFVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVREL
EVGVLGNVFGEASPVGEVRYEAPFYDYETKYTPGRAELLIPAPLDPGTQE
TVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRL
FEAGGVAYPELLRRLVELALTHHH

3D structure

• PDB: 6u1d d-Alanine-d-alanine ligase as a model for the activation of ATP-grasp enzymes by monovalent cations.
• Chain: A
• Resolution: 1.9 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): V16 L19 H82 E226 R268 G288 T292
• Catalytic site (residue number reindexed from 1): V18 L21 H84 E228 R270 G290 T294
• Enzyme Commision number: 6.3.2.4: D-alanine--D-alanine ligase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	DAL	A	E13 H82 Y229 R268	E15 H84 Y231 R270
BS02	DAL	A	K228 R268 G288 S293	K230 R270 G290 S295
BS03	MG	A	D270 E282	D272 E284
BS04	MG	A	E282 N284	E284 N286
BS05	ATP	A	K116 F151 K153 G158 S159 S160 I163 E189 A191 L192 E197 Y223 K228 F272 N281 E282	K118 F153 K155 G160 S161 S162 I165 E191 A193 L194 E199 Y225 K230 F274 N283 E284

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

External links

• PDB: RCSB:6u1d, PDBe:6u1d, PDBj:6u1d
• PDBsum: 6u1d
• PubMed: 32335509
• UniProt: Q5SHZ3|DDL_THET8 D-alanine--D-alanine ligase (Gene Name=ddl)