4MMD - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF LEUBAT (DELTA6 MUTANT) IN COMPLEX WITH (S)-DULOXETINE

Authors :   H. Wang, E. Gouaux

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

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   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, 9)

No.	Name	Count	Type	Full Name
1	29E	2	Ligand/Ion	(3S)-N-METHYL-3-(NAPHTHALEN-1-YLOXY)-3-(THIOPHEN-2-YL)PROPAN-1-AMINE
2	BOG	3	Ligand/Ion	B-OCTYLGLUCOSIDE
3	NA	4	Ligand/Ion	SODIUM ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	29E	1	Ligand/Ion	(3S)-N-METHYL-3-(NAPHTHALEN-1-YLOXY)-3-(THIOPHEN-2-YL)PROPAN-1-AMINE
2	BOG	3	Ligand/Ion	B-OCTYLGLUCOSIDE
3	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	29E	1	Ligand/Ion	(3S)-N-METHYL-3-(NAPHTHALEN-1-YLOXY)-3-(THIOPHEN-2-YL)PROPAN-1-AMINE
2	BOG	-1	Ligand/Ion	B-OCTYLGLUCOSIDE
3	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 3 (2, 5)

No.	Name	Count	Type	Full Name
1	29E	2	Ligand/Ion	(3S)-N-METHYL-3-(NAPHTHALEN-1-YLOXY)-3-(THIOPHEN-2-YL)PROPAN-1-AMINE
2	BOG	3	Ligand/Ion	B-OCTYLGLUCOSIDE
3	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (9, 9)

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 , ASN A:27 , SER A:254 , ASN A:286 , GLU A:290 , HOH A:714	BINDING SITE FOR RESIDUE NA A 602
3	AC3	SOFTWARE	TYR A:21 , ALA A:22 , ASP A:24 , PRO A:101 , VAL A:104 , ALA A:105 , TYR A:108 , PHE A:253 , SER A:254 , GLY A:256 , PHE A:259 , SER A:356 , GLY A:359 , HOH A:748 , HOH A:761	BINDING SITE FOR RESIDUE 29E A 603
4	AC4	SOFTWARE	MET A:476 , GLU A:477 , GLU A:478 , THR A:479 , VAL A:483 , TRP A:484 , ARG A:487 , BOG A:606 , ILE B:161	BINDING SITE FOR RESIDUE BOG A 604
5	AC5	SOFTWARE	LYS A:163 , PRO A:164 , SER A:165 , LEU A:166 , TYR A:169 , PHE A:395	BINDING SITE FOR RESIDUE BOG A 605
6	AC6	SOFTWARE	TRP A:484 , PHE A:488 , BOG A:604 , HOH A:729 , HIS B:391	BINDING SITE FOR RESIDUE BOG A 606
7	AC7	SOFTWARE	GLY B:20 , VAL B:23 , ALA B:351 , THR B:354 , SER B:355	BINDING SITE FOR RESIDUE NA B 601
8	AC8	SOFTWARE	ALA B:22 , ASN B:27 , SER B:254 , ASN B:286 , GLU B:290 , HOH B:726	BINDING SITE FOR RESIDUE NA B 602
9	AC9	SOFTWARE	TYR B:21 , ALA B:22 , ASP B:24 , PRO B:101 , VAL B:104 , ALA B:105 , TYR B:107 , TYR B:108 , PHE B:253 , SER B:254 , GLY B:256 , PHE B:259 , SER B:356 , GLY B:359	BINDING SITE FOR RESIDUE 29E B 603

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

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 4MMD)

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

(no "Exon" information available for 4MMD)

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:504
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4mmda_ A: Na(+):neurotransmitter symporter homologue LeuT                                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.ee..eehhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4mmd A   5 REHWATRLGLILAMAGYAVDLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIEWAMGRYGGAQGHGTTPAIFYLLWRNRFAKILGVFGLWIPLVVAIYYVYIESWTLGFAIKFLVGLVPEPPTDPDSILRPFKEFLYSYIGVPKGDEPILKPSLFAYIVFLITMFINVSILIRGISKGIERFAKIAMPTLFILAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDPGVWIAAVGQIFFSLGLGFGAIITFASYVRKDQDIVLSGLTAATLNEKAEVILGGSISIPAAVAFFGVANAVAIAKAGAFNLGFITLPAIFSQTAGGTFLGFLWFFLLFFAGLTSSIAGMQPMIAFLEDELKLSRKHAVLWTAAIVFFSAHLVMFLNKSLDEMDFWAGTIGVVFFGLTELIIFFWIFGADKAWEEINRGGIIKVPRIYYYVMRYITPAFLAVLLVVWAREYIPKIMEETHWTVWITRFYIIGLFLFLTFLVFLAERRRNHE 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       477       487       497       507    
                                                                                                                                                        131|                                                                                                                                                                                                                                                                                                                                                                                        
                                                                                                                                                         135

Chain B from PDB  Type:PROTEIN  Length:504
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4mmdb_ B: Na(+):neurotransmitter symporter homologue LeuT                                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.ee..eehhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4mmd B   5 REHWATRLGLILAMAGYAVDLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIEWAMGRYGGAQGHGTTPAIFYLLWRNRFAKILGVFGLWIPLVVAIYYVYIESWTLGFAIKFLVGLVPEPPTDPDSILRPFKEFLYSYIGVPKGDEPILKPSLFAYIVFLITMFINVSILIRGISKGIERFAKIAMPTLFILAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDPGVWIAAVGQIFFSLGLGFGAIITFASYVRKDQDIVLSGLTAATLNEKAEVILGGSISIPAAVAFFGVANAVAIAKAGAFNLGFITLPAIFSQTAGGTFLGFLWFFLLFFAGLTSSIAGMQPMIAFLEDELKLSRKHAVLWTAAIVFFSAHLVMFLNKSLDEMDFWAGTIGVVFFGLTELIIFFWIFGADKAWEEINRGGIIKVPRIYYYVMRYITPAFLAVLLVVWAREYIPKIMEETHWTVWITRFYIIGLFLFLTFLVFLAERRRNHE 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       477       487       497       507    
                                                                                                                                                        131|                                                                                                                                                                                                                                                                                                                                                                                        
                                                                                                                                                         135

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	d4mmda_	A:
1b	d4mmdb_	B:

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		29E	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		BOG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ 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, 9)

Sites (9, 9)

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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