2JK5 - JenaLib

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Title :   POTASSIUM CHANNEL KCSA IN COMPLEX WITH TETRABUTYLAMMONIUM IN HIGH K

Authors :   M. J. Lenaeus, P. J. Focia, T. Wagner, A. Gross

Date :   15 Aug 08 (Deposition) - 17 Nov 09 (Release) - 03 Sep 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,B,C  (4x)

Keywords :   Immune System-Metal Transport Complex, Quaternary Ammonium, Protein-Antibody Fab Complex, Ionic Channel, Ion Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. J. Lenaeus, D. Burdette, T. Wagner, P. J. Focia, A. Gross
Structures Of Kcsa In Complex With Symmetrical Quaternary Ammonium Compounds Reveal A Hydrophobic Binding Site.
Biochemistry V. 53 5365 2014
PubMed-ID: 25093676 | Reference-DOI: 10.1021/BI500525S

Molecule 1 - ANTIBODY FAB FRAGMENT LIGHT CHAIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Common	:	HOUSE MOUSE
	Expression System Taxid	:	10090
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	HYBRIDOMA

Molecule 2 - ANTIBODY FAB FRAGMENT HEAVY CHAIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Common	:	HOUSE MOUSE
	Expression System Taxid	:	10090
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	HYBRIDOMA

Molecule 3 - VOLTAGE-GATED POTASSIUM CHANNEL
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 1-124
	Organism Scientific	:	STREPTOMYCES LIVIDANS
	Organism Taxid	:	1916
	Synonym	:	KCSA POTASSIUM CHANNEL

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (4x)	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 11)

No.	Name	Count	Type	Full Name
1	CO	1	Ligand/Ion	COBALT (II) ION
2	F09	1	Ligand/Ion	NONAN-1-OL
3	HP6	1	Ligand/Ion	HEPTANE
4	K	6	Ligand/Ion	POTASSIUM ION
5	L2C	1	Ligand/Ion	(2S)-3-HYDROXY-2-(NONANOYLOXY)PROPYL LAURATE
6	TBA	1	Ligand/Ion	TETRABUTYLAMMONIUM ION

Biological Unit 1 (4, 16)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION
2	F09	4	Ligand/Ion	NONAN-1-OL
3	HP6	4	Ligand/Ion	HEPTANE
4	K	-1	Ligand/Ion	POTASSIUM ION
5	L2C	4	Ligand/Ion	(2S)-3-HYDROXY-2-(NONANOYLOXY)PROPYL LAURATE
6	TBA	4	Ligand/Ion	TETRABUTYLAMMONIUM ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS C:124 , HOH C:2048	BINDING SITE FOR RESIDUE CO C1124
02	AC2	SOFTWARE	GLY C:77 , TYR C:78 , K C:1126	BINDING SITE FOR RESIDUE K C1125
03	AC3	SOFTWARE	VAL C:76 , GLY C:77 , K C:1125 , K C:1127	BINDING SITE FOR RESIDUE K C1126
04	AC4	SOFTWARE	THR C:75 , VAL C:76 , K C:1126 , K C:1128	BINDING SITE FOR RESIDUE K C1127
05	AC5	SOFTWARE	THR C:75 , K C:1127	BINDING SITE FOR RESIDUE K C1128
06	AC6	SOFTWARE	HOH C:2012	BINDING SITE FOR RESIDUE K C1129
07	AC7	SOFTWARE	HOH A:2026 , LEU C:46 , HP6 C:1134	BINDING SITE FOR RESIDUE F09 C1131
08	AC8	SOFTWARE	PRO C:63 , VAL C:84 , ARG C:89 , HOH C:2051	BINDING SITE FOR RESIDUE L2C C1132
09	AC9	SOFTWARE	THR C:74 , THR C:75	BINDING SITE FOR RESIDUE TBA C1133
10	BC1	SOFTWARE	LEU C:46 , F09 C:1131	BINDING SITE FOR RESIDUE HP6 C1134

Asymmetric Unit

No.	Residues
1	A:22	-	A:96
2	A:145	-	A:200
3	B:23	-	B:88
4	B:134	-	B:194

Asymmetric Unit

No.	Residues
1	Phe A:151	-	Pro A:152
2	Glu A:153	-	Pro A:154
3	Trp A:193	-	Pro A:194
4	Ser B:7	-	Pro B:8
5	Trp B:94	-	Pro B:95
6	Tyr B:140	-	Pro B:141

(no "SAP(SNP)/Variant" information available for 2JK5)

(no "PROSITE Motif" information available for 2JK5)

(no "Exon" information available for 2JK5)

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:219
                                                                                                                                                                                                                                                           
               SCOP domains d2jk5a1 A:1-118 Immunoglobulin heavy chain variable domain, VH                                                        d2jk5a2 A:119-219 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains 2jk5A01 A:1-118 Immunoglobulins                                                                                       2jk5A02 A:119-217 Immunoglobulins                                                                  -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...eeee.....eeeeeee........eeeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee.....eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh.....ee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jk5 A   1 QVQLQQPGAELVKPGASVKLSCKASGYTFTSDWIHWVKQRPGHGLEWIGEIIPSYGRANYNEKIQKKATLTADKSSSTAFMQLSSLTSEDSAVYYCARERGDGYFAVWGAGTTVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSSWPSETVTCNVAHPASSTKVDKKIVPRD 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain B from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains d2jk5b1 B:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d2jk5b2 B:108-212 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------2jk5B02 B:109-211 Immunoglobulins                                                                      - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jk5 B   1 DILLTQSPAILSVSPGERVSFSCRASQSIGTDIHWYQQRTNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIANYYCQQSNRWPFTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain C from PDB  Type:PROTEIN  Length:103
 aligned with KCSA_STRLI | P0A334 from UniProtKB/Swiss-Prot  Length:160

    Alignment length:103
                                    31        41        51        61        71        81        91       101       111       121   
           KCSA_STRLI    22 SALHWRAAGAATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVETATTVGYGDLYPVTLWGRLVAVVVMVAGITSFGLVTAALATWFVGREQERRGH 124
               SCOP domains d2jk5c_ C: automated matches                                                                            SCOP domains
               CATH domains 2jk5C00 C:22-124  [code=1.10.287.70, no name defined]                                                   CATH domains
               Pfam domains -----------Ion_trans_2-2jk5C01 C:33-116                                                        -------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 2jk5 C  22 SALHWRAAGAATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVETATTVGYGDLYPVTLWGRCVAVVVMVAGITSFGLVTAALATWFVGREQERRGH 124
                                    31        41        51        61        71        81        91       101       111       121

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Helix Hairpins (718)

Homologous Superfamily: [code=1.10.287.70, no name defined] (106)

Mouse (Mus musculus) (5)

2jk5C00

C:22-124

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Mouse (Mus musculus) (152)

2a	2jk5B02	B:109-211
2b	2jk5A02	A:119-217
2c	2jk5A01	A:1-118

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ion_channel (150)

Family: Ion_trans_2 (35)

Streptomyces lividans (16)

Ion_trans_2-2jk5C01

C:33-116

Asymmetric Unit(hide GO term definitions)

Chain C (KCSA_STRLI | P0A334)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0005249	voltage-gated potassium channel activity	Enables the transmembrane transfer of a potassium ion by a voltage-gated channel. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
biological process
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0071805	potassium ion transmembrane transport	A process in which a potassium ion is transported from one side of a membrane to the other.
	GO:0006813	potassium ion transport	The directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0008076	voltage-gated potassium channel complex	A protein complex that forms a transmembrane channel through which potassium ions may cross a cell membrane in response to changes in membrane potential.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		CO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		F09	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Cis Peptide Bonds
		Glu A:153 - Pro A:154	[ RasMol ]
		Phe A:151 - Pro A:152	[ RasMol ]
		Ser B:7 - Pro B:8	[ RasMol ]
		Trp A:193 - Pro A:194	[ RasMol ]
		Trp B:94 - Pro B:95	[ RasMol ]
		Tyr B:140 - Pro B:141	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Access by PDB/NDB ID
	2jk5
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		Orientation in Membranes	:	OPM
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	KCSA_STRLI \| P0A334
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		Disease Information	:	OMIM

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		Interatomic Contacts of Structural Units	:	CSU
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1bl8	POTASSIUM CHANNEL (KCSA) FROM STREPTOMYCES LIVIDANS
1f6g	POTASSIUM CHANNEL (KCSA) FULL-LENGTH FOLD
1j95	KCSA POTASSIUM CHANNEL WITH TBA ( TETRABUTYLAMMONIUM) ANDPOTASSIUM
1jq1	POTASSIUM CHANNEL (KCSA) OPEN GATE MODEL
1jq2	POTASSIUM CHANNEL (KCSA) OPEN GATE MODEL
1jvm	KCSA POTASSIUM CHANNEL WITH TBA ( TETRABUTYLAMMONIUM) ANDRUBIDIUM
1k4c	POTASSIUM CHANNEL KCSA-FAB COMPLEX IN HIGH CONCENTRATION OFK+
1k4d	POTASSIUM CHANNEL KCSA-FAB COMPLEX IN LOW CONCENTRATION OFK+
1r3i	POTASSIUM CHANNEL KCSA-FAB COMPLEX IN RB+
1r3j	POTASSIUM CHANNEL KCSA-FAB COMPLEX IN HIGH CONCENTRATION OFTL+
1r3k	POTASSIUM CHANNEL KCSA-FAB COMPLEX IN LOW CONCENTRATION OFTL+
1r3l	POTASSIUM CHANNEL KCSA-FAB COMPLEX IN CS+
1zwi	STRUCTURE OF MUTANT KCSA POTASSIUM CHANNEL
2a9h	NMR STRUCTURAL STUDIES OF A POTASSIUM CHANNEL /CHARYBDOTOXIN COMPLEX
2atk	STRUCTURE OF A MUTANT KCSA K+ CHANNEL
2bob	POTASSIUM CHANNEL KCSA-FAB COMPLEX IN THALLIUM WITH TETRABUTYLAMMONIUM (TBA)
2boc	POTASSIUM CHANNEL KCSA-FAB COMPLEX IN THALLIUM WITH TETRAETHYLARSONIUM (TEAS)
2h8p	STRUCTURE OF A K CHANNEL WITH AN AMIDE TO ESTERSUBSTITUTION IN THE SELECTIVITY FILTER
2hg5	CS+ COMPLEX OF A K CHANNEL WITH AN AMIDE TO ESTERSUBSTITUTION IN THE SELECTIVITY FILTER
2ih1	ION SELECTIVITY IN A SEMI-SYNTHETIC K+ CHANNEL LOCKED INTHE CONDUCTIVE CONFORMATION
2ih3	ION SELECTIVITY IN A SEMI-SYNTHETIC K+ CHANNEL LOCKED INTHE CONDUCTIVE CONFORMATION
2w0f	POTASSIUM CHANNEL KCSA-FAB COMPLEX WITH TETRAOCTYLAMMONIUM
4uuj	POTASSIUM CHANNEL KCSA-FAB COMPLEX WITH TETRAHEXYLAMMONIUM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 11)

Sites (10, 10)

SS Bonds (4, 4)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (5, 5)

CATH Domains (2, 4)

Pfam Domains (1, 1)

Gene Ontology (10, 10)

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