Structure of PDB 2vd6 Chain A Binding Site BS01

Receptor Information

>2vd6 Chain A (length=461) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

GDHGSPDSYRSPLASRYASPEMCFVFSDRYKFRTWRQLWLWLAEAEQTLG
LPITDEQIQEMKSNLENIDFKMAAEEEKRLRHDVMAHVHTFGHCCPKAAG
IIHLGATSCYVGDNTDLIILRNALDLLLPKLARVISRLADFAKERASLPT
LGFTHFQPAQLTTVGKRCCLWIQDLCMDLQNLKRVRDDLRFRGVKGTTGT
QASFLQLFEGDDHKVEQLDKMVTEKAGFKRAFIITGQTYTRKVDIEVLSV
LASLGASVHKICTDIRLLANLKEMEEPFEPYKRNPMRSERCCSLARHLMT
LVMDPLQTASVQWFERTLDDSANRRICLAEAFLTADTILNTLQNISEGLV
VYPKVIERRIRQELPFMATENIIMAMVKAGGSRQDCHEKIRVLSQQAASV
VKQEGGDNDLIERIQVDAYFSPIHSQLDHLLDPSSFTGRASQQVQRFLEE
EVYPLLKPYES

Ligand information

Ligand ID

AMP

InChI

InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1

InChIKey

UDMBCSSLTHHNCD-KQYNXXCUSA-N

SMILES

Software	SMILES
CACTVS 3.370	Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370	Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.6	c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
ACDLabs 12.01	O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.6	c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N

Formula

C10 H14 N5 O7 P

Name

ADENOSINE MONOPHOSPHATE

PDB chain

2vd6 Chain A Residue 1000 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

Global view

Local view

Structure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

PDB	2vd6 Human Adenylosuccinate Lyase in Complex with its Substrate N6-(1,2-Dicarboxyethyl)-AMP, and its Products AMP and Fumarate.
Resolution	2.0 Å
Binding residue (original residue number in PDB)	R85 H86 Q241 L331 S334 R338
Binding residue (residue number reindexed from 1)	R81 H82 Q237 L318 S321 R325
Annotation score	5

Enzymatic activity

Catalytic site (original residue number in PDB)	H86 T158 H159 K295 E302
Catalytic site (residue number reindexed from 1)	H82 T154 H155 K282 E289
Enzyme Commision number	4.3.2.2: adenylosuccinate lyase.

Gene Ontology

	Molecular Function
GO:0003824	catalytic activity
GO:0004018	N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity
GO:0016829	lyase activity
GO:0042802	identical protein binding
GO:0070626	(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido) succinate lyase (fumarate-forming) activity

	Biological Process
GO:0001666	response to hypoxia
GO:0006164	purine nucleotide biosynthetic process
GO:0006167	AMP biosynthetic process
GO:0006177	GMP biosynthetic process
GO:0006189	'de novo' IMP biosynthetic process
GO:0007584	response to nutrient
GO:0009060	aerobic respiration
GO:0009152	purine ribonucleotide biosynthetic process
GO:0009168	purine ribonucleoside monophosphate biosynthetic process
GO:0014850	response to muscle activity
GO:0042594	response to starvation
GO:0044208	'de novo' AMP biosynthetic process
GO:0044209	AMP salvage
GO:0097294	'de novo' XMP biosynthetic process

	Cellular Component
GO:0005829	cytosol
GO:0032991	protein-containing complex

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:2vd6, PDBe:2vd6, PDBj:2vd6
PDBsum	2vd6
PubMed
UniProt	P30566\|PUR8_HUMAN Adenylosuccinate lyase (Gene Name=ADSL)

[Back to BioLiP]