Structure of PDB 5jf8 Chain A

Receptor sequence
>5jf8A (length=203) Species: 1311 (Streptococcus agalactiae) [Search protein sequence]
AAIDKLVKASHLIDMNDIIREGNPTLRKVAEEVTFPLSEKEEILGEKMMQ
FLKHSQDPIMAEKLGLRGGVGLAAPQLDISKRIIAVLVPNVEDAQGNPPK
EAYSLQEVMYNPKVVSHSVQDAALSDGEGCLSVDREVPGYVVRHARVTIE
YFDKTGEKHRLKLKGYNSIVVQHEIDHIDGIMFYDRINEKNPFAVKEGLL
ILE
3D structure
PDB5jf8 A unique peptide deformylase platform to rationally design and challenge novel active compounds.
ChainA
Resolution1.8 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) G72 Q77 C131 L132 H174 E175 H178
Catalytic site (residue number reindexed from 1) G71 Q76 C130 L131 H173 E174 H177
Enzyme Commision number 3.5.1.88: peptide deformylase.
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 PN3 A G72 Q77 E129 G130 C131 H174 E175 H178 G71 Q76 E128 G129 C130 H173 E174 H177 MOAD: Ki=1428nM
PDBbind-CN: -logKd/Ki=5.85,Ki=1428nM
BS02 ZN A C131 H174 H178 C130 H173 H177
BS03 ZN A H12 D18 H11 D17
BS04 ZN A E43 E47 E42 E46
Gene Ontology
Molecular Function
GO:0016787 hydrolase activity
GO:0042586 peptide deformylase activity
GO:0046872 metal ion binding
Biological Process
GO:0006412 translation
GO:0018206 peptidyl-methionine modification

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Molecular Function
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Biological Process
External links
PDB RCSB:5jf8, PDBe:5jf8, PDBj:5jf8
PDBsum5jf8
PubMed27762275
UniProtQ8E378|DEF_STRA3 Peptide deformylase (Gene Name=def)

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