Structure of PDB 6czd Chain A

Receptor sequence
>6czdA (length=227) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence]
GGTILVVTGTGTGVGKTVVCAALASAARQAGIDVAVCKPVQTGTARGDDD
LAEVGRLAGVTQLAGLARYPQPMAPAAAAEHAGMALPARDQIVRLIADLD
RPGRLTLVEGAGGLLVELAEPGVTLRDVAVDVAAAALVVVTADLGTLNHT
KLTLEALAAQQVSCAGLVIGSWPDPPGLVAASNRSALARIAMVRAALPAG
AASLDAGDFAAMSAAAFDRNWVAGLVG
3D structure
PDB6czd Precipitant-ligand exchange technique reveals the ADP binding mode in Mycobacterium tuberculosis dethiobiotin synthetase.
ChainA
Resolution2.4 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) T11 G12 K15 T16 K37 T41 G54 E108
Catalytic site (residue number reindexed from 1) T12 G13 K16 T17 K38 T42 G55 E109
Enzyme Commision number 6.3.3.3: dethiobiotin 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 MG A T16 D49 E108 T17 D50 E109
BS02 ADP A T11 G12 V13 G14 K15 T16 M72 A73 E108 A110 G111 T12 G13 V14 G15 K16 T17 M73 A74 E109 A111 G112 PDBbind-CN: -logKd/Ki=3.85,Ki=0.14mM
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004141 dethiobiotin synthase activity
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0009102 biotin biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6czd, PDBe:6czd, PDBj:6czd
PDBsum6czd
PubMed30289406
UniProtP9WPQ5|BIOD_MYCTU Dethiobiotin synthetase BioD (Gene Name=bioD)

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