4MMC - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF LEUBAT (DELTA6 MUTANT) IN COMPLEX WITH DESVENLAFAXINE

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./Biol. Unit : A

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
	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
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	29J	2	Ligand/Ion	4-[(1R)-2-(DIMETHYLAMINO)-1-(1-HYDROXYCYCLOHEXYL)ETHYL]PHENOL
2	BOG	2	Ligand/Ion	B-OCTYLGLUCOSIDE
3	NA	2	Ligand/Ion	SODIUM ION

Asymmetric Unit (6, 6)

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 , HOH A:704	BINDING SITE FOR RESIDUE NA A 602
3	AC3	SOFTWARE	TYR A:21 , ASP A:24 , VAL A:104 , TYR A:107 , TYR A:108 , PHE A:253 , GLY A:256 , PHE A:259 , SER A:355 , GLY A:359 , ASP A:404 , 29J A:604	BINDING SITE FOR RESIDUE 29J A 603
4	AC4	SOFTWARE	PHE A:320 , LEU A:400 , ASP A:401 , ASP A:404 , THR A:409 , 29J A:603	BINDING SITE FOR RESIDUE 29J A 604
5	AC5	SOFTWARE	LYS A:163 , HIS A:391 , PHE A:395 , LYS A:431 , BOG A:606	BINDING SITE FOR RESIDUE BOG A 605
6	AC6	SOFTWARE	ILE A:161 , LEU A:396 , LYS A:431 , BOG A:605	BINDING SITE FOR RESIDUE BOG A 606

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

Asymmetric/Biological Unit

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

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

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

(no "Exon" information available for 4MMC)

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:504
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4mmca_ A: Na(+):neurotransmitter symporter homologue LeuT                                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.ee..eehhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4mmc 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

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/Biological 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)

d4mmca_

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
	Complete Structure
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	Ligands, Modified Residues, Ions
		29J	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		BOG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ 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
		Pro A:130 - Pro A:131	[ RasMol ]

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	4mmc
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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
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		Interatomic Contacts of Structural Units	:	CSU
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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