Structure of PDB 3dhy Chain D Binding Site BS02

Receptor Information

>3dhy Chain D (length=485) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

LTPDVRNGIDFKIADLSLADFGRKELRIAEHEMPGLMSLRREYAEVQPLK
GARISGSLHMTVQTAVLIETLTALGAEVRWASCNIFSTQDHAAAAVVVGP
HGTPDEPKGVPVFAWKGETLEEYWWAAEQMLTWPDPDKPANMILDDGGDA
TMLVLRGMQYEKAGVVPPAEEDDPAEWKVFLNLLRTRFETDKDKWTKIAE
SVKGVTEETTTGVLRLYQFAAAGDLAFPAINVNDSVTKSKFDNKYGTRHS
LIDGINRGTDALIGGKKVLICGYGDVGKGCAEAMKGQGARVSVTEIDPIN
ALQAMMEGFDVVTVEEAIGDADIVVTATGNKDIIMLEHIKAMKDHAILGN
IGHFDNEIDMAGLERSGATRVNVKPQVDLWTFGDTGRSIIVLSEGRLLNL
GNATGHPSFVMSNSFANQTIAQIELWTKNDEYDNEVYRLPKHLDEKVARI
HVEALGGHLTKLTKEQAEYLGVDVEGPYKPDHYRY

Ligand information

Ligand ID

3DH

InChI

InChI=1S/C12H17N5O3S/c1-2-21-3-6-8(18)9(19)12(20-6)17-5-16-7-10(13)14-4-15-11(7)17/h4-6,8-9,12,18-19H,2-3H2,1H3,(H2,13,14,15)/t6-,8-,9-,12-/m1/s1

InChIKey

HMXHURAGFHWODC-WOUKDFQISA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	CCSC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
OpenEye OEToolkits 1.5.0	CCSCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.341	CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.341	CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 10.04	n2c1c(ncnc1n(c2)C3OC(C(O)C3O)CSCC)N

Formula

C12 H17 N5 O3 S

Name

5'-S-ethyl-5'-thioadenosine;
S-adenosylethane

PDB chain

3dhy Chain D Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	3dhy Crystal structures of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with substrate and inhibitors.
Resolution	2.0 Å
Binding residue (original residue number in PDB)	L68 H69 T71 D156 E218 T219 D252 L407 L410 G415 H416 M421
Binding residue (residue number reindexed from 1)	L58 H59 T61 D146 E208 T209 D242 L397 L400 G405 H406 M411
Annotation score	3

Enzymatic activity

Catalytic site (original residue number in PDB)	H69 S92 S97 D156 E218 N243 K248 D252 N253 T257 H363 H416 S424 Q428
Catalytic site (residue number reindexed from 1)	H59 S82 S87 D146 E208 N233 K238 D242 N243 T247 H353 H406 S414 Q418
Enzyme Commision number	3.13.2.1: adenosylhomocysteinase.

Gene Ontology

	Molecular Function
GO:0004013	adenosylhomocysteinase activity
GO:0005515	protein binding
GO:0016787	hydrolase activity
GO:0035375	zymogen binding
GO:0070403	NAD+ binding

	Biological Process
GO:0006730	one-carbon metabolic process
GO:0009087	methionine catabolic process
GO:0033353	S-adenosylmethionine cycle
GO:0035635	entry of bacterium into host cell
GO:0044650	adhesion of symbiont to host cell
GO:0046085	adenosine metabolic process
GO:0071269	L-homocysteine biosynthetic process

	Cellular Component
GO:0005576	extracellular region
GO:0005737	cytoplasm
GO:0005829	cytosol
GO:0005886	plasma membrane
GO:0009274	peptidoglycan-based cell wall

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Molecular Function

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Cellular Component

External links

PDB	RCSB:3dhy, PDBe:3dhy, PDBj:3dhy
PDBsum	3dhy
PubMed	18815415
UniProt	P9WGV3\|SAHH_MYCTU Adenosylhomocysteinase (Gene Name=ahcY)

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