Structure of PDB 2ynd Chain B

Receptor sequence

>2yndB (length=385) Species: 5855 (Plasmodium vivax) [Search protein sequence]

IDYKFWYTQPVPKINDEFNESVNEPFISDNKVEDVRKDEYKLPPGYSWYV
CDVKDEKDRSEIYTLLTDNYVEDDDNIFRFNYSAEFLLWALTSPNYLKTW
HIGVKYDASNKLIGFISAIPTDICIHKRTIKMAEVNFLCVHKTLRSKRLA
PVLIKEITRRINLENIWQAIYTAGVYLPKPVSDARYYHRSINVKKLIEIG
FSSLNSRLTMSRAIKLYRVEDTLNIKNMRLMKKKDVEGVHKLLGSYLEQF
NLYAVFTKEEIAHWFLPIENVIYTYVNEENGKIKDMISFYSLPSQILGND
KYSTLNAAYSFYNVTTTATFKQLMQDAILLAKRNNFDVFNALEVMQNKSV
FEDLKFGEGDGSLKYYLYNWKCASFAPAHVGIVLL

3D structure

PDB

2ynd Validation of N-Myristoyltransferase as an Antimalarial Drug Target Using an Integrated Chemical Biology Approach.

Chain

Resolution

1.89 Å

3D
structure

Catalytic site residues are labeled in the structure
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Enzymatic activity

Catalytic site (original residue number in PDB)	N161 F162 L163 T197 L410
Catalytic site (residue number reindexed from 1)	N136 F137 L138 T172 L385
Enzyme Commision number	2.3.1.97: glycylpeptide N-tetradecanoyltransferase.

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	NHW	B	Y28 F30 W31 Y95 N161 L163 C164 V165 R170 S171 R173 L174 A175 P176 I179 T183 I186 W192 Q193 Y196 T197 A198 L202 Y393	Y3 F5 W6 Y70 N136 L138 C139 V140 R145 S146 R148 L149 A150 P151 I154 T158 I161 W167 Q168 Y171 T172 A173 L177 Y368
BS02	646	B	D98 F103 F105 G199 Y211 H213 F226 S319 Y334 L388 L410	D73 F78 F80 G174 Y186 H188 F201 S294 Y309 L363 L385	MOAD: Ki=32nM
BS03	MG	B	L169 R170 S171 K172 L174	L144 R145 S146 K147 L149

Gene Ontology

	Molecular Function
GO:0004379	glycylpeptide N-tetradecanoyltransferase activity
GO:0016746	acyltransferase activity
GO:0046872	metal ion binding

	Biological Process
GO:0006499	N-terminal protein myristoylation
GO:0018008	N-terminal peptidyl-glycine N-myristoylation

	Cellular Component
GO:0005737	cytoplasm

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Molecular Function

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Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:2ynd, PDBe:2ynd, PDBj:2ynd
PDBsum	2ynd
PubMed	24451586
UniProt	A5K1A2

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