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(-) Description

Title :  CRYSTAL STRUCTURE OF KV1.2-2.1 PADDLE CHIMERA CHANNEL IN COMPLEX WITH LYS27MET MUTANT OF CHARYBDOTOXIN
 
Authors :  A. Banerjee, A. Lee, E. Campbell, R. Mackinnon
Date :  23 Mar 13  (Deposition) - 12 Jun 13  (Release) - 12 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.54
Chains :  Asym. Unit :  A,B,G,H,Y
Biol. Unit 1:  A,B  (4x)
Biol. Unit 2:  G (4x),H (4x),Y (1x)
Keywords :  Potassium Channel, Pore Blocking Toxin, Protein-Protein Complex, Trans-Enhanced Dissociation Effect, Transport Protein-Toxin Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Banerjee, A. Lee, E. Campbell, R. Mackinnon
Structure Of A Pore-Blocking Toxin In Complex With A Eukaryotic Voltage-Dependent K(+) Channel.
Elife V. 2 00594 2013
PubMed-ID: 23705070  |  Reference-DOI: 10.7554/ELIFE.00594

(-) Compounds

Molecule 1 - VOLTAGE-GATED POTASSIUM CHANNEL SUBUNIT BETA-2
    ChainsA, G
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System Taxid4922
    GeneCKBETA2, KCNAB2, KCNB3
    Organism CommonBROWN RAT,RAT,RATS
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymK(+) CHANNEL SUBUNIT BETA-2, KV-BETA-2
 
Molecule 2 - POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY A MEMBER 2, POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY B MEMBER 1
    ChainsB, H
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System Taxid4922
    GeneKCNA2, KCNB1
    Organism CommonBROWN RAT,RAT,RATS
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymRAK, RBK2, RCK5, VOLTAGE-GATED POTASSIUM CHANNEL SUBUNIT KV1.2, DELAYED RECTIFIER POTASSIUM CHANNEL 1, DRK1, VOLTAGE-GATED POTASSIUM CHANNEL SUBUNIT KV2.1
 
Molecule 3 - POTASSIUM CHANNEL TOXIN ALPHA-KTX 1.1
    ChainsY
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentCHARYBDOTOXIN
    MutationYES
    Organism CommonYELLOW SCORPION
    Organism ScientificLEIURUS QUINQUESTRIATUS HEBRAEUS
    Organism Taxid6884
    SynonymCHTX-LQ1, CHTX-A, CHARYBDOTOXIN, CHTX

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit ABGHY
Biological Unit 1 (4x)AB   
Biological Unit 2 (4x)  G (4x)H (4x)Y (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 28)

Asymmetric Unit (4, 28)
No.NameCountTypeFull Name
1K8Ligand/IonPOTASSIUM ION
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3PCA1Mod. Amino AcidPYROGLUTAMIC ACID
4PGW17Ligand/Ion(1R)-2-{[(S)-{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(HEXADECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE
Biological Unit 1 (2, 68)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3PCA-1Mod. Amino AcidPYROGLUTAMIC ACID
4PGW64Ligand/Ion(1R)-2-{[(S)-{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(HEXADECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2NAP-1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3PCA-1Mod. Amino AcidPYROGLUTAMIC ACID
4PGW-1Ligand/Ion(1R)-2-{[(S)-{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(HEXADECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:55 , THR A:56 , TRP A:57 , GLN A:63 , ASP A:85 , TYR A:90 , LYS A:118 , ASN A:158 , SER A:188 , ARG A:189 , GLN A:214 , TRP A:243 , SER A:244 , PRO A:245 , LEU A:246 , ALA A:247 , CYS A:248 , GLY A:249 , LYS A:254 , TYR A:262 , SER A:263 , ARG A:264 , PRO A:304 , LEU A:322 , GLY A:323 , SER A:325 , GLN A:329 , GLU A:332 , ASN A:333 , HOH A:1140 , HOH A:1141 , HOH A:1167 , HOH A:1230BINDING SITE FOR RESIDUE NAP A 1001
02AC2SOFTWAREGLY B:372 , TYR B:373BINDING SITE FOR RESIDUE K B 501
03AC3SOFTWAREVAL B:371 , GLY B:372 , K B:503BINDING SITE FOR RESIDUE K B 502
04AC4SOFTWARETHR B:370 , VAL B:371 , K B:502BINDING SITE FOR RESIDUE K B 503
05AC5SOFTWARETHR B:370BINDING SITE FOR RESIDUE K B 504
06AC6SOFTWAREILE B:328 , PRO B:358 , PHE B:361 , ILE B:381 , LYS B:384 , SER B:388 , PGW B:509 , PGW B:510BINDING SITE FOR RESIDUE PGW B 505
07AC7SOFTWAREPGW B:507BINDING SITE FOR RESIDUE PGW B 506
08AC8SOFTWAREPGW B:506BINDING SITE FOR RESIDUE PGW B 507
09AC9SOFTWAREILE B:385 , PGW B:505BINDING SITE FOR RESIDUE PGW B 509
10BC1SOFTWAREVAL B:178 , PGW B:505BINDING SITE FOR RESIDUE PGW B 510
11BC2SOFTWAREILE B:328 , THR B:397 , PGW B:512 , PGW B:516BINDING SITE FOR RESIDUE PGW B 511
12BC3SOFTWAREMET B:321 , GLY B:325 , PGW B:511BINDING SITE FOR RESIDUE PGW B 512
13BC4SOFTWAREPHE B:222BINDING SITE FOR RESIDUE PGW B 514
14BC5SOFTWARESER B:307 , LYS B:308 , GLY B:309 , ARG B:322 , GLY B:325 , LEU B:326BINDING SITE FOR RESIDUE PGW B 515
15BC6SOFTWAREPGW B:511BINDING SITE FOR RESIDUE PGW B 516
16BC7SOFTWAREPHE B:301 , LYS B:308 , LEU B:310 , GLN B:311 , GLY B:314 , ARG B:415 , GLU B:416BINDING SITE FOR RESIDUE PGW B 517
17BC8SOFTWAREILE B:257 , ILE B:264BINDING SITE FOR RESIDUE PGW B 519
18BC9SOFTWAREPHE B:218BINDING SITE FOR RESIDUE PGW B 520
19CC1SOFTWAREGLY G:55 , THR G:56 , TRP G:57 , GLN G:63 , ASP G:85 , TYR G:90 , LYS G:118 , ASN G:158 , SER G:188 , ARG G:189 , GLN G:214 , TRP G:243 , SER G:244 , PRO G:245 , LEU G:246 , CYS G:248 , GLY G:249 , SER G:252 , LYS G:254 , TYR G:262 , SER G:263 , ARG G:264 , PRO G:304 , LEU G:322 , GLY G:323 , ALA G:324 , SER G:325 , GLN G:329 , GLU G:332 , ASN G:333 , HOH G:1135 , HOH G:1136 , HOH G:1150BINDING SITE FOR RESIDUE NAP G 1001
20CC2SOFTWAREGLY H:372 , TYR H:373 , K H:502BINDING SITE FOR RESIDUE K H 501
21CC3SOFTWAREVAL H:371 , GLY H:372 , K H:501 , K H:503BINDING SITE FOR RESIDUE K H 502
22CC4SOFTWARETHR H:370 , VAL H:371 , K H:502 , K H:504BINDING SITE FOR RESIDUE K H 503
23CC5SOFTWARETHR H:370 , K H:503BINDING SITE FOR RESIDUE K H 504
24CC6SOFTWAREPRO H:358 , TRP H:362 , VAL H:365 , ILE H:381 , LYS H:384 , SER H:388BINDING SITE FOR RESIDUE PGW H 505

(-) SS Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Y:7 -Y:28
2Y:13 -Y:33
3Y:13 -Y:17
4Y:17 -Y:35
5Y:17 -Y:33

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JTD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JTD)

(-) Sequences/Alignments

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:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4jtda_ A: Voltage-dependent K+ channel beta subunit                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee......eee.eeee.........hhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhh.hhhhheeeeee.....hhhhh..hhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhh.....eee.......hhhhhhhhhhhhhhhh.eeee...hhhhhhhh.........hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh....eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jtd A  36 LQFYRNLGKSGLRVSCLGLGTWVTFGGQITDEMAEHLMTLAYDNGINLFDTAEVYAAGKAEVVLGNIIKKKGWRRSSLVITTKIFWGGKAETERGLSRKHIIEGLKASLERLQLEYVDVVFANRPDPNTPMEETVRAMTHVINQGMAMYWGTSRWSSMEIMEAYSVARQFNLIPPICEQAEYHMFQREKVEVQLPELFHKIGVGAMTWSPLACGIVSGKYDSGIPPYSRASLKGYQWLKDKILSEEGRRQQAKLKELQAIAERLGCTLPQLAIAWCLRNEGVSSVLLGASNAEQLMENIGAIQVLPKLSSSIVHEIDSILGNKPYS 361
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355      

Chain B from PDB  Type:PROTEIN  Length:386
                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..eeeeeehhhhh........hhhhhh..ee....eeee..hhhhhhhhhhhhhh..........hhhhhhhhhhhh..hhhhhhhhhhhh..............hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh..........hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jtd B  32 SERVVINISGLRFETQLKTLAQFPETLLGDPKKRMRYFDPLRNEYFFDRNRPSFDAILYYYQSGGRLRRPVNVPLDIFSEEIRFYELGEEAMEMFREDEGYIKEEERPLPENEFQRQVWLLFEYPESSGPARIIAIVSVMVILISIVSFCLETLPIFRDENEDMHGGGVTFHTYSQSTIGYQQSTSFTDPFFIVETLCIIWFSFEFLVRFFACPSKAGFFTNIMNIIDIVAIIPYYVTIFLTESNKSVLQFQNVRRVVQIFRIMRILRIFKLSRHSKGLQILGQTLKASMRELGLLIFFLFIGVILFSSAVYFAEADERDSQFPSIPDAFWWAVVSMTTVGYGDMVPTTIGGKIVGSLCAIAGVLTIALPVPVIVSNFNYFYHRET 417
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411      

Chain G from PDB  Type:PROTEIN  Length:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4jtdg_ G: Voltage-dependent K+ channel beta subunit                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee......eee.eeee.........hhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhh.hhhhheeeeee.....hhhhh..hhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhh.eeeee..hhhhhhhh.........hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhh...hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jtd G  36 LQFYRNLGKSGLRVSCLGLGTWVTFGGQITDEMAEHLMTLAYDNGINLFDTAEVYAAGKAEVVLGNIIKKKGWRRSSLVITTKIFWGGKAETERGLSRKHIIEGLKASLERLQLEYVDVVFANRPDPNTPMEETVRAMTHVINQGMAMYWGTSRWSSMEIMEAYSVARQFNLIPPICEQAEYHMFQREKVEVQLPELFHKIGVGAMTWSPLACGIVSGKYDSGIPPYSRASLKGYQWLKDKILSEEGRRQQAKLKELQAIAERLGCTLPQLAIAWCLRNEGVSSVLLGASNAEQLMENIGAIQVLPKLSSSIVHEIDSILGNKPYS 361
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355      

Chain H from PDB  Type:PROTEIN  Length:363
                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..eeeeeehhhhh........hhhhhh..ee....eeee..hhhhhhhhhhhhhhh.........hhhhhhhhhhhh..hhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhh.........................hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh.hhhhhhh........hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jtd H  32 SERVVINISGLRFETQLKTLAQFPETLLGDPKKRMRYFDPLRNEYFFDRNRPSFDAILYYYQSGGRLRRPVNVPLDIFSEEIRFYELGEEAMEMFREDEGFQRQVWLLFEYPESSGPARIIAIVSVMVILISIVSFCLETLPIFRDEFHTYSQSTIGYQQSTSFTDPFFIVETLCIIWFSFEFLVRFFACPSKAGFFTNIMNIIDIVAIIPYYVTIFLTESNKSVLQFQNVRRVVQIFRIMRILRIFKLSRHSKGLQILGQTLKASMRELGLLIFFLFIGVILFSSAVYFAEADERDSQFPSIPDAFWWAVVSMTTVGYGDMVPTTIGGKIVGSLCAIAGVLTIALPVPVIVSNFNYFYHRET 417
                                    41        51        61        71        81        91       101       111       121       131|      154       164       174       184      |204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414   
                                                                                                                             131|                                           191|                                                                                                                                                                                                                       
                                                                                                                              145                                            202                                                                                                                                                                                                                       

Chain Y from PDB  Type:PROTEIN  Length:37
                                                                     
               SCOP domains d4jtdy_ Y: automated matches          SCOP domains
               CATH domains ------------------------------------- CATH domains
               Pfam domains ------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhh........ee......ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------- PROSITE
                 Transcript ------------------------------------- Transcript
                 4jtd Y   1 xFTNVSCTTSKECWSVCQRLHNTSRGMCMNKKCRCYS  37
                            |       10        20        30       
                            1-PCA                                

   Legend:   → Mismatch (orange background)
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  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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 3)

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(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (89, 135)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        KAX11_LEIQH | P134871bah 1cmr 2a9h 2crd 4jta 4jtc
        KCAB2_RAT | P624831exb 1qrq 2a79 2r9r 3eau 3eb3 3eb4 3lnm 3lut 4jta 4jtc
        KCNA2_RAT | P631421dsx 1qdv 1qdw 2a79 2r9r 3lnm 3lut 4jta 4jtc
        KCNB1_RAT | P153872r9r 3lnm 4jta 4jtc

(-) Related Entries Specified in the PDB File

2crd STRUCTURE OF THE TOXIN ONLY
2r9r STRUCTURE OF THE CHANNEL ONLY
4jta STRUCTURE OF THE KV1.2-2.1 PADDLE CHIMERA CHANNEL WITH SELENOMETHIONINE DERIVATIVE OF CHARYBDOTOXIN
4jtc