4MM4 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF LEUBAT (DELTA13 MUTANT) IN COMPLEX WITH PAROXETINE

Authors :   H. Wang, E. Gouaux

Date :   08 Sep 13 (Deposition) - 16 Oct 13 (Release) - 20 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.89

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

Keywords :   Leut Fold, Transporter, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Wang, A. Goehring, K. H. Wang, A. Penmatsa, R. Ressler, E. Gouaux
Structural Basis For Action By Diverse Antidepressants On Biogenic Amine Transporters.
Nature V. 503 141 2013
PubMed-ID: 24121440 | Reference-DOI: 10.1038/NATURE12648

Molecule 1 - TRANSPORTER
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	SNF, AQ_2077
	Mutation	:	YES
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	224324
	Strain	:	VF5

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	8PR	2	Ligand/Ion	PAROXETINE
2	CL	1	Ligand/Ion	CHLORIDE ION
3	NA	4	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	8PR	1	Ligand/Ion	PAROXETINE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	8PR	1	Ligand/Ion	PAROXETINE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	8PR	2	Ligand/Ion	PAROXETINE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:20 , VAL A:23 , ALA A:351 , THR A:354 , SER A:355	BINDING SITE FOR RESIDUE NA A 601
2	AC2	SOFTWARE	ALA A:22 , ASP A:24 , ASN A:27 , SER A:254 , ASN A:286 , 8PR A:603 , HOH A:701	BINDING SITE FOR RESIDUE NA A 602
3	AC3	SOFTWARE	TYR A:21 , ALA A:22 , ASP A:24 , PRO A:101 , ALA A:105 , TYR A:107 , TYR A:108 , PHE A:253 , SER A:254 , PHE A:259 , SER A:355 , SER A:356 , GLY A:359 , ASP A:404 , THR A:408 , NA A:602	BINDING SITE FOR RESIDUE 8PR A 603
4	AC4	SOFTWARE	GLY B:20 , VAL B:23 , ALA B:351 , THR B:354 , SER B:355	BINDING SITE FOR RESIDUE NA B 601
5	AC5	SOFTWARE	ALA B:22 , ASP B:24 , ASN B:27 , SER B:254 , ASN B:286 , 8PR B:603	BINDING SITE FOR RESIDUE NA B 602
6	AC6	SOFTWARE	TYR B:21 , ALA B:22 , ASP B:24 , PRO B:101 , ALA B:105 , TYR B:107 , TYR B:108 , PHE B:253 , SER B:254 , PHE B:259 , SER B:355 , SER B:356 , GLY B:359 , ASP B:404 , THR B:408 , NA B:602	BINDING SITE FOR RESIDUE 8PR B 603
7	AC7	SOFTWARE	TYR B:47 , SER B:254 , ASN B:286 , GLU B:287 , SER B:290	BINDING SITE FOR RESIDUE CL B 604

(no "SS Bond" information available for 4MM4)

Asymmetric Unit

No.	Residues
1	Pro A:130	-	Pro A:131
2	Pro B:130	-	Pro B:131

(no "SAP(SNP)/Variant" information available for 4MM4)

(no "PROSITE Motif" information available for 4MM4)

(no "Exon" information available for 4MM4)

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:497
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4mm4a_ A: Na(+):neurotransmitter symporter homologue LeuT                                                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh..ee..eehhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mm4 A   5 REHWATRLGLILAMAGYAVDLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIEWAMGRYGGAQGHGTTPAIFYLLWRNRFAKILGVFGLWIPLVVASYYVYIESWTLGFAIKFLVGLVPEPPTDPDSILRPFKEFLYSYIGVPKGDEPILKPSLFAYIVFLITMFINVSILIRGISKGIERFAKIAMPTLFILAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDPGVWIAAVGQIFFSLGLGFGVLITFASYVRKDQDIVLSGLTAATLNEKASVILGGSISIPAAVAFFGVANAVAIAKAGAFNLGFITLPAIFSQTAGGTFLGFLWFFLLFFAGLTSSIAGMQGMIAFLEDELKLSRKHAVLWTAAIVFFSAHLVMFLNKSLDEMDFWATGIGVVFFGLTELIIFFWIFGADKAWEEINRGGIIKVPRIYYYVMRYITPAFLAVLLVVWAREYTHWTVWITRFYIIGLFLFLTFLVFLAERRRNHE 511
                                    14        24        34        44        54        64        74        84        94       104       114       124      |137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467   ||  484       494       504       
                                                                                                                                                        131|                                                                                                                                                                                                                                                                                                                                             471|                                
                                                                                                                                                         135                                                                                                                                                                                                                                                                                                                                              479

Chain B from PDB  Type:PROTEIN  Length:499
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4mm4b_ B: Na(+):neurotransmitter symporter homologue LeuT                                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh..ee..eehhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mm4 B   5 REHWATRLGLILAMAGYAVDLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIEWAMGRYGGAQGHGTTPAIFYLLWRNRFAKILGVFGLWIPLVVASYYVYIESWTLGFAIKFLVGLVPEPPTDPDSILRPFKEFLYSYIGVPKGDEPILKPSLFAYIVFLITMFINVSILIRGISKGIERFAKIAMPTLFILAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDPGVWIAAVGQIFFSLGLGFGVLITFASYVRKDQDIVLSGLTAATLNEKASVILGGSISIPAAVAFFGVANAVAIAKAGAFNLGFITLPAIFSQTAGGTFLGFLWFFLLFFAGLTSSIAGMQGMIAFLEDELKLSRKHAVLWTAAIVFFSAHLVMFLNKSLDEMDFWATGIGVVFFGLTELIIFFWIFGADKAWEEINRGGIIKVPRIYYYVMRYITPAFLAVLLVVWAREYIPTHWTVWITRFYIIGLFLFLTFLVFLAERRRNHE 511
                                    14        24        34        44        54        64        74        84        94       104       114       124      |137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467     ||482       492       502         
                                                                                                                                                        131|                                                                                                                                                                                                                                                                                                                                               473|                                
                                                                                                                                                         135                                                                                                                                                                                                                                                                                                                                                479

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Membrane and cell surface proteins and peptides (2046)

Fold: SNF-like (42)

Superfamily: SNF-like (42)

Family: SNF-like (42)

Protein domain: Na(+):neurotransmitter symporter homologue LeuT (35)

Aquifex aeolicus [TaxId: 63363] (35)

1a	d4mm4a_	A:
1b	d4mm4b_	B:

(no "CATH Domain" information available for 4MM4)

(no "Pfam Domain" information available for 4MM4)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
	Complete Structure
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	Ligands, Modified Residues, Ions
		8PR	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Pro A:130 - Pro A:131	[ RasMol ]
		Pro B:130 - Pro B:131	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (9, 9)

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