Structure of PDB 5j5d Chain A

Receptor sequence
>5j5dA (length=297) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence]
VGFDVAARLGTLLTAMVTPFSGDGSLDTATAARLANHLVDQGCDGLVVSG
TTGESPTTTDGEKIELLRAVLEAVGDRARVIAGAGTYDTAHSIRLAKACA
AEGAHGLLVVTPYYSKPPQRGLQAHFTAVADATELPMLLYDIPGRSAVPI
EPDTIRALASHPNIVGVKDAKADLHSGAQIMADTGLAYYSGDDALNLPWL
AMGATGFISVIAHLAAGQLRELLSAFGSGDIATARKINIAVAPLCNAMSR
LGGVTLSKAGLRLQGIDVGDPRLPQVAATPEQIDALAADMRAASVLR
3D structure
PDB5j5d Inhibition of Mycobacterium tuberculosis dihydrodipicolinate synthase by alpha-ketopimelic acid and its other structural analogues
ChainA
Resolution2.4 Å
3D
structure
Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
Enzymatic activity
Catalytic site (original residue number in PDB) T54 Y117 Y143 R148 K171 I211
Catalytic site (residue number reindexed from 1) T51 Y114 Y140 R145 K168 I208
Enzyme Commision number 4.3.3.7: 4-hydroxy-tetrahydrodipicolinate synthase.
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 6GT A A18 T54 T55 Y143 R148 K171 G194 A15 T51 T52 Y140 R145 K168 G191 PDBbind-CN: -logKd/Ki=4.68,IC50=21uM
Gene Ontology
Molecular Function
GO:0008840 4-hydroxy-tetrahydrodipicolinate synthase activity
GO:0016829 lyase activity
Biological Process
GO:0009085 lysine biosynthetic process
GO:0009089 lysine biosynthetic process via diaminopimelate
GO:0019877 diaminopimelate biosynthetic process
GO:0044281 small molecule metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5j5d, PDBe:5j5d, PDBj:5j5d
PDBsum5j5d
PubMed27501775
UniProtP9WP25|DAPA_MYCTU 4-hydroxy-tetrahydrodipicolinate synthase (Gene Name=dapA)

[Back to BioLiP]