4XP5 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   X-RAY STRUCTURE OF DROSOPHILA DOPAMINE TRANSPORTER BOUND TO COCAINE ANALOGUE-RTI55

Authors :   E. Gouaux, A. Penmatsa, K. Wang

Date :   16 Jan 15 (Deposition) - 06 May 15 (Release) - 03 Jun 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.30

Chains :   Asym./Biol. Unit : A,H,L

Keywords :   Integral Membrane Protein, Membrane Protein-Transport Protein Complex, Transport Protein-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. H. Wang, A. Penmatsa, E. Gouaux
Neurotransmitter And Psychostimulant Recognition By The Dopamine Transporter.
Nature V. 521 322 2015
PubMed-ID: 25970245 | Reference-DOI: 10.1038/NATURE14431

Molecule 1 - DOPAMINE TRANSPORTER, ISOFORM B
	Chains	:	A
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Taxid	:	9606
	Gene	:	DAT, DMEL_CG8380
	Mutation	:	YES
	Organism Common	:	FRUIT FLY
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Organism Taxid	:	7227

Molecule 2 - ANTIBODY FRAGMENT HEAVY CHAIN-PROTEIN, 9D5-HEAVY CHAIN
	Chains	:	L
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Cell Line	:	GNTI-HEK293S
	Expression System Taxid	:	10090
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 3 - IGHG PROTEIN
	Chains	:	H
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		1	2	3
Asymmetric/Biological Unit	:	A	H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 8)

No.	Name	Count	Type	Full Name
1	42F	1	Ligand/Ion	METHYL (1R,2S,3S,5S)-3-(4-IODOPHENYL)-8-METHYL-8-AZABICYCLO[3.2.1]OCTANE-2-CARBOXYLATE
2	CL	1	Ligand/Ion	CHLORIDE ION
3	CLR	2	Ligand/Ion	CHOLESTEROL
4	MAL	1	Ligand/Ion	MALTOSE
5	NA	2	Ligand/Ion	SODIUM ION
6	P4G	1	Ligand/Ion	1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:133 , PHE A:136 , ALA A:137 , PRO A:144 , TYR A:215 , TYR A:219 , ASP A:238	binding site for residue MAL A 601
2	AC2	SOFTWARE	PHE A:43 , ASP A:46 , ASP A:121 , TYR A:124 , PHE A:319 , SER A:320 , LEU A:321 , GLY A:322 , PHE A:325 , NA A:606	binding site for residue 42F A 602
3	AC3	SOFTWARE	LEU A:73 , ILE A:78 , TYR A:518 , TRP A:519	binding site for residue CLR A 603
4	AC4	SOFTWARE	ARG A:476 , TYR A:481	binding site for residue P4G A 604
5	AC5	SOFTWARE	VAL A:34 , LEU A:37 , LEU A:38 , LEU A:270 , TYR A:273 , ILE A:351 , ILE A:358	binding site for residue CLR A 605
6	AC6	SOFTWARE	ALA A:44 , ASN A:49 , SER A:320 , ASN A:352 , 42F A:602	binding site for residue NA A 606
7	AC7	SOFTWARE	TYR A:69 , GLN A:316 , SER A:320 , SER A:356	binding site for residue CL A 607
8	AC8	SOFTWARE	GLY A:42 , VAL A:45 , LEU A:417 , ASP A:420 , SER A:421	binding site for residue NA A 608

Asymmetric/Biological Unit

No.	Residues
1	A:148	-	A:157
2	H:22	-	H:96
3	H:146	-	H:201
4	L:23	-	L:89
5	L:135	-	L:195

Asymmetric/Biological Unit

No.	Residues
1	Asp A:25	-	Glu A:26
2	Arg A:598	-	Asp A:599
3	Ser L:7	-	Pro L:8
4	Tyr L:95	-	Pro L:96
5	Tyr L:141	-	Pro L:142
6	Arg H:98	-	Gly H:99
7	Asp H:136	-	Thr H:137
8	Phe H:152	-	Pro H:153
9	Glu H:154	-	Pro H:155
10	Trp H:194	-	Pro H:195

(no "SAP(SNP)/Variant" information available for 4XP5)

(no "PROSITE Motif" information available for 4XP5)

(no "Exon" information available for 4XP5)

Asymmetric/Biological 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:534
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh.....................hhhhhhhhhh..hhhhh.........hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh....ee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xp5 A  25 DERETWSGKVDFLLSVIGFAVDLANVWRFPYLCYKNGGGAFLVPYGIMLAVGGIPLFYMELALGQHNRKGAITCWGRLVPLFKGIGYAVVLIAFYVDFYYNVIIAWSLRFFFASFTNSLPWTSCNNIWNTPNCRPFEGHVEGFQSAASEYFNRYILELNRSEGIHDLGAIKWDMALCLLIVYLICYFSLWKGISTSGKVVWFTALFPYAVLLILLIRGLTLPGSFLGIQYYLTPNFSAIYKAEVWVDAATQVFFSLGPGFGVLLAYASYNKYHNNVYKDALLTSFINSATSFIAGFVIFSVLGYMAHTLGVRIEDVATEGPGLVFVVYPAAIATMPASTFWALIFFMMLATLGLDSSFGGSEAIITALSDEFPKIKRNRELFVAGLFSLYFVVGLASCTQGGFYFFHLLDRYAAGYSILVAVFFEAIAVSWIYGTNRFSEDIRDMIGFPPGRYWQVCWRFVAPIFLLFITVYGLIGYEPLTYADYVYPSWANALGWCIAGSSVVMIPAVAIFKLLSTPGSLRQRFTILTTPWRD 599
                                    34        44        54        64        74        84        94       104       114       124       134       144       154      |205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595    
                                                                                                                                                                  161|                                                                                                                                                                                                                                                                                                                                                                                                            
                                                                                                                                                                   203

Chain H from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..ee......eeeeeee........eeeeee.....eeeeeee......eee.......ee..ee....eeeeee...hhhhheeeeeee..hhhhh..ee...eeeee........eeeee............eeeeeeeee.....eeee........eeeeeeeee..eeeeeeeee............eeeee....eeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xp5 H   1 EVQLVESGGGLVKPGGSLKLSCAASGFTFSSYAMSWVRQSPEKRLEWVAEISSGGRYIYYSDTVTGRFTISRDNARNILHLEMSSLRSEDTAMYYCARGEVRQRGFDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee........eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee.....hhhh.eeeeeeeeeee.....eeeeee..eee...eeeeee........eeeeeeeeeehhhhh....eeeeeee..eeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xp5 L   1 ENVLTQSPAIMSTSPGEKVTMTCRASSSVGSSYLHWYQQKSGASPKLWIYSTSNLASGVPARFSGSGSGTSYSLTISSVEAEDAATYYCQQFSGYPLTFGSGTKLEMKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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 '\|'

(no "SCOP Domain" information available for 4XP5)

(no "CATH Domain" information available for 4XP5)

(no "Pfam Domain" information available for 4XP5)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
		42F	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CLR	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MAL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		P4G	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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		AC2	[ RasMol ]	+environment [ RasMol ]
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		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Arg A:598 - Asp A:599	[ RasMol ]
		Arg H:98 - Gly H:99	[ RasMol ]
		Asp A:25 - Glu A:26	[ RasMol ]
		Asp H:136 - Thr H:137	[ RasMol ]
		Glu H:154 - Pro H:155	[ RasMol ]
		Phe H:152 - Pro H:153	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Trp H:194 - Pro H:195	[ RasMol ]
		Tyr L:141 - Pro L:142	[ RasMol ]
		Tyr L:95 - Pro L:96	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 4XP5)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 8)

Sites (8, 8)

SS Bonds (5, 5)

Cis Peptide Bonds (10, 10)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (22, 22)

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