5U2H - JenaLib

Title :   CRYSTAL STRUCTURE OF THE ATP-GATED P2X7 ION CHANNEL BOUND TO ATP AND ALLOSTERIC ANTAGONIST A804598

Authors :   A. Karasawa, T. Kawate

Date :   30 Nov 16 (Deposition) - 04 Jan 17 (Release) - 04 Jan 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.90

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (3x)
Biol. Unit 2: B  (3x)

Keywords :   Membrane Protein: Atp-Gated Ion Channel: Agonist And Allosteric Antagonist Bound: Closed State, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Karasawa, T. Kawate
Structural Basis For Subtype-Specific Inhibition Of The P2X Receptor.
Elife V. 5 2016
PubMed-ID: 27935479 | Reference-DOI: 10.7554/ELIFE.22153

Compounds

Molecule 1 - P2X PURINOCEPTOR
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Taxid	:	7108
	Gene	:	P2RX7
	Organism Common	:	GIANT PANDA
	Organism Scientific	:	AILUROPODA MELANOLEUCA
	Organism Taxid	:	9646
	Other Details	:	THE N- AND C-TERMINI, AND SEVERAL OTHER LOOP REGIONS ARE DISORDERED AND THE ELECTRON DENSITY WAS NOT WELL-DEFINED.

Structural Features

Chains, Units

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (3x)	:	A
Biological Unit 2 (3x)	:		B

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 8)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	7S1	2	Ligand/Ion	N-CYANO-N'-[(1R)-1-PHENYLETHYL]-N''-QUINOLIN-5-YLGUANIDINE
2	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
3	NAG	5	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (2, 9)

No.	Name	Count	Type	Full Name
1	7S1	3	Ligand/Ion	N-CYANO-N'-[(1R)-1-PHENYLETHYL]-N''-QUINOLIN-5-YLGUANIDINE
2	ATP	-1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
3	NAG	6	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (3, 15)

No.	Name	Count	Type	Full Name
1	7S1	3	Ligand/Ion	N-CYANO-N'-[(1R)-1-PHENYLETHYL]-N''-QUINOLIN-5-YLGUANIDINE
2	ATP	3	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
3	NAG	9	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:92 , PHE A:95 , PHE A:103 , MET A:105 , PHE A:108 , TYR A:295 , TYR A:298 , VAL A:312	binding site for residue LIG A 403
2	AC2	SOFTWARE	ASP B:92 , THR B:94 , PHE B:108 , LYS B:110 , TYR B:295 , TYR B:298	binding site for residue LIG B 404
3	AC3	SOFTWARE	LYS B:64 , LYS B:66 , THR B:189 , LEU B:191 , ILE B:228 , TYR B:288 , ASN B:292	binding site for residue ATP B 405
4	AC4	SOFTWARE	ASN A:183 , SER A:184 , ASN A:187	binding site for Poly-Saccharide residues NAG A 401 through NAG A 402 bound to ASN A 187
5	AC5	SOFTWARE	ASN B:183 , SER B:184 , ASN B:187	binding site for Poly-Saccharide residues NAG B 401 through NAG B 402 bound to ASN B 187
6	AC6	SOFTWARE	ASN B:202	binding site for Mono-Saccharide NAG B 403 bound to ASN B 202

SS Bonds (9, 9)

Asymmetric Unit

No.	Residues
1	A:119	-	A:168
2	A:129	-	A:152
3	A:135	-	A:162
4	A:216	-	A:226
5	A:260	-	A:269
6	B:119	-	B:168
7	B:129	-	B:152
8	B:135	-	B:162
9	B:260	-	B:269

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:307
                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh..eeee..eeeeeeeee..eeeeeeeee..eeeeeeeeehhhhhh......eeeeeeeeeeeeeeeeeeee................eee.......eeeeeeee.....eeeeeeeee.............hhhhh..eeeeeeeeee....eeee...............eeehhhhhhhhh.hhhhhhhhheeeeeeeeee...........eeeeeee.........eeeeeeeeeee..eeeeeeeeeeeeeeeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u2h A  34 HALVFSYISFALISDKRYQKKEPLISSVHTKVKGIAEVKAEILENGMKKMVSGVFDTADYTFPLQGNSFFVMTNFIKTEGQQQGLCPDFPTARTICSSDRGCKKGRMDPQSKGIQTGRCVVYKERLKTCEVSAWCPIEEVKDAPRPALLNSAENFTVLIKNNIDFPGHNYTTRNITCTFHKTQNPQCPIFRLGDIFQETGDSFSDVAIQGGIMGIEIYWDCNLDGWFHHCRPKYSFRRLDDKTTYPGYNFRYAKYYKENNVEKRTLIKVFGIRFDILVFGTGGKFNVIQLAVYIGSVISYFGLATVF 350
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203   ||  219       229       239       249       259       269       279   ||  293       303       313       323       333       343       
                                                                                                                                                                                                       207|                                                                  283|                                                              
                                                                                                                                                                                                        214                                                                   288

Chain B from PDB  Type:PROTEIN  Length:299
                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..eeeeeeeee..eeeeee........eeeeee............eeeeeeeeeeeeeeeeeeee..........hhhhh.eee.......eeeeeeee.....eeeeeeeee.............hhhhh..eeeeeeeee..............................eeehhhhhhhhh.hhhhhhhhheeeeeeeeee............eeeee...............eeeeeeeeee..eeeeeeeeeeeeeeeeeeeee.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u2h B  34 HALVFSYISFALISDPLISSVHTKVKGIAEVKAEILENGMKKMVSGVFDTADYTFPLQGNSFFVMTNFIKTEGQQQGLCPDFPTARTICSSDRGCKKGRMDPQSKGIQTGRCVVYKERLKTCEVSAWCPIEEVKDAPRPALLNSAENFTVLIKNNIDFPGHNYTTRNILPGVNITCTFHKTQNPQCPIFRLGDIFQETGDSFSDVAIQGGIMGIEIYWDCNLDGWFHHCRPKYSFRRLDDKTTSESLYPGYNFRYAKYYKENNVEKRTLIKVFGIRFDILVFGTLAVYIGSVISYFGLA 347
                                    43    ||  60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320   ||  338         
                                         48|                                                                                                                                                                                                                                                                         324|              
                                          56                                                                                                                                                                                                                                                                          333

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (100, 100)

Visualization

Interactive Views

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		7S1	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ATP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Cys A:168 - Pro A:169	[ RasMol ]
		Cys B:168 - Pro B:169	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	5u2h
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	G1M6C4_AILME \| G1M6C4
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	G1M6C4_AILME \| G1M6C4
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description