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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN POTASSIUM CHANNEL KV BETA-SUBUNIT (KCNAB2)
 
Authors :  P. Wennerstrand, I. Johannsson, E. Ugochukwu, K. Kavanagh, A. Edwards C. Arrowsmith, L. Williams, M. Sundstrom, K. Guo, F. Von Delft, U. Opp Structural Genomics Consortium (Sgc)
Date :  25 May 05  (Deposition) - 07 Jun 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Biol. Unit 2:  A  (8x)
Keywords :  Potassium Channel, Kv Beta-Subunit, Human, Aldo-Keto Reductase, Structural Genomics, Sgc, Structural Genomics Consortium, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Wennerstrand, I. Johannsson, E. Ugochukwu, K. Kavanagh, A. Edwards, C. Arrowsmith, L. Williams, M. Sundstrom, K. Guo, F. Von Delft, U. Oppermann
Crystal Structure Of Human Potassium Channel Kv Beta-Subuni (Kcnab2)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - VOLTAGE-GATED POTASSIUM CHANNEL BETA-2 SUBUNIT
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidP11
    Expression System StrainBL21-DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneORIGENE
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymK+, CHANNEL BETA-2 SUBUNIT, KV-BETA-2, HKVBETA2, AKR6A5

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (4x)A
Biological Unit 2 (8x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NAP8Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:201 , GLU A:202 , LYS A:210BINDING SITE FOR RESIDUE CL A 347
2AC2SOFTWAREASN A:192BINDING SITE FOR RESIDUE CL A 349
3AC3SOFTWAREMET A:152 , GLU A:183 , LYS A:221BINDING SITE FOR RESIDUE CL A 350
4AC4SOFTWAREGLY A:41 , THR A:42 , TRP A:43 , GLN A:49 , ASP A:71 , TYR A:76 , LYS A:104 , ASN A:144 , SER A:174 , ARG A:175 , GLN A:200 , TRP A:229 , SER A:230 , PRO A:231 , LEU A:232 , ALA A:233 , CYS A:234 , GLY A:235 , SER A:238 , LYS A:240 , SER A:249 , ARG A:250 , LEU A:307 , LEU A:308 , GLY A:309 , SER A:311 , GLN A:315 , GLU A:318 , ASN A:319 , HOH A:801 , HOH A:807 , HOH A:812 , HOH A:814 , HOH A:823 , HOH A:825 , HOH A:997BINDING SITE FOR RESIDUE NAP A 800

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZSX)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ZSX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048747E88KKCAB2_HUMANPolymorphism2229003AE74K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048747E88KKCAB2_HUMANPolymorphism2229003AE74K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048747E88KKCAB2_HUMANPolymorphism2229003AE74K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ZSX)

(-) Exons   (14, 14)

Asymmetric Unit (14, 14)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003780972aENSE00001476308chr1:6052423-6052848426KCAB2_HUMAN-00--
1.10ENST0000037809710ENSE00002163766chr1:6100577-6100705129KCAB2_HUMAN1-26260--
1.12aENST0000037809712aENSE00000734983chr1:6101891-610193242KCAB2_HUMAN26-40151A:-1-264
1.14cENST0000037809714cENSE00000734942chr1:6132815-613285844KCAB2_HUMAN40-55161A:26-4116
1.15aENST0000037809715aENSE00001620859chr1:6133793-613383038KCAB2_HUMAN55-67131A:41-5313
1.16ENST0000037809716ENSE00000378098chr1:6142255-614233480KCAB2_HUMAN68-94271A:54-8027
1.17bENST0000037809717bENSE00000734886chr1:6145264-614530845KCAB2_HUMAN94-109161A:80-9516
1.19ENST0000037809719ENSE00000734884chr1:6147527-614757145KCAB2_HUMAN109-124161A:95-11016
1.20ENST0000037809720ENSE00000734882chr1:6149068-614911144KCAB2_HUMAN124-139161A:110-12516
1.21ENST0000037809721ENSE00000734879chr1:6150449-615053587KCAB2_HUMAN139-168301A:125-15430
1.23ENST0000037809723ENSE00000734876chr1:6154460-615454586KCAB2_HUMAN168-196291A:154-18229
1.24ENST0000037809724ENSE00001615557chr1:6155383-6155503121KCAB2_HUMAN197-237411A:183-22341
1.25bENST0000037809725bENSE00000734870chr1:6155590-615568495KCAB2_HUMAN237-268321A:223-25432
1.26bENST0000037809726bENSE00000734868chr1:6156696-6156816121KCAB2_HUMAN269-309411A:255-29541
1.27aENST0000037809727aENSE00000734866chr1:6157329-615741789KCAB2_HUMAN309-338301A:295-32430
1.28eENST0000037809728eENSE00001476246chr1:6158545-61612532709KCAB2_HUMAN339-367291A:325-34521

(-) 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:323
 aligned with KCAB2_HUMAN | Q13303 from UniProtKB/Swiss-Prot  Length:367

    Alignment length:323
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356   
          KCAB2_HUMAN    37 QFYRNLGKSGLRVSCLGLGTWVTFGGQITDEMAEQLMTLAYDNGINLFDTAEVYAAGKAEVVLGNIIKKKGWRRSSLVITTKIFWGGKAETERGLSRKHIIEGLKASLERLQLEYVDVVFANRPDPNTPMEETVRAMTHVINQGMAMYWGTSRWSSMEIMEAYSVARQFNLTPPICEQAEYHMFQREKVEVQLPELFHKIGVGAMTWSPLACGIVSGKYDSGIPPYSRASLKGYQWLKDKILSEEGRRQQAKLKELQAIAERLGCTLPQLAIAWCLRNEGVSSVLLGASNADQLMENIGAIQVLPKLSSSIIHEIDSILGNKP 359
               SCOP domains d1zsxa_ A: automated matches                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1zsxA00 A:-1-345 NADP-dependent oxidoreductase                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains --------------Aldo_ket_red-1zsxA01 A:37-332                                                                                                                                                                                                                                                                           ------------- Pfam domains
         Sec.struct. author ..eee......eee.eeee.........hhhhhhhhhhhhhhh...eee...hhhhhhhhhhhhhhhhhhh.hhhhheeeeee.....hhhhh..hhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhh.eeeee..hhhhhhhh.........hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------K------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.12--------------Exon 1.15a   Exon 1.16  PDB: A:54-80    --------------Exon 1.19       --------------Exon 1.21  PDB: A:125-154     ----------------------------Exon 1.24  PDB: A:183-223                -------------------------------Exon 1.26b  PDB: A:255-295               -----------------------------Exon 1.28e            Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.14c      --------------------------------------Exon 1.17b      --------------Exon 1.20       ----------------------------Exon 1.23  PDB: A:154-182    ----------------------------------------Exon 1.25b  PDB: A:223-254      ----------------------------------------Exon 1.27a  PDB: A:295-324    --------------------- Transcript 1 (2)
                 1zsx A  -1 QFYRNLGKSGLRVSCLGLGTWVTFGGQITDEMAEQLMTLAYDNGINLFDTAEVYAAGKAEVVLGNIIKKKGWRRSSLVITTKIFWGGKAETERGLSRKHIIEGLKASLERLQLEYVDVVFANRPDPNTPMEETVRAMTHVINQGMAMYWGTSRWSSMEIMEAYSVARQFNLTPPICEQAEYHMFQREKVEVQLPELFHKIGVGAMTWSPLACGIVSGKYDSGIPPYSRASLKGYQWLKDKILSEEGRRQQAKLKELQAIAERLGCTLPQLAIAWCLRNEGVSSVLLGASNADQLMENIGAIQVLPKLSSSIIHEIDSILGNKP 345
                             ||     32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342   
                             0|                                                                                                                                                                                                                                                                                                                                
                             25                                                                                                                                                                                                                                                                                                                                

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (34, 34)

Asymmetric Unit(hide GO term definitions)
Chain A   (KCAB2_HUMAN | Q13303)
molecular function
    GO:0004033    aldo-keto reductase (NADP) activity    Catalysis of the reaction: an alcohol + NADP+ = an aldehyde or a ketone + NADPH + H+.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0015459    potassium channel regulator activity    Modulates potassium channel activity via direct interaction interaction with a potassium channel (binding or modification).
    GO:0005244    voltage-gated ion channel activity    Enables the transmembrane transfer of an ion by a voltage-gated channel. An ion is an atom or group of atoms carrying an electric charge by virtue of having gained or lost one or more electrons. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
    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:0070995    NADPH oxidation    A metabolic process that results in the oxidation of reduced nicotinamide adenine dinucleotide, NADPH, to the oxidized form, NADP.
    GO:0002244    hematopoietic progenitor cell differentiation    The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells.
    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:0050905    neuromuscular process    Any process pertaining to the functions of the nervous and muscular systems of an organism.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    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:0034765    regulation of ion transmembrane transport    Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other.
    GO:1901379    regulation of potassium ion transmembrane transport    Any process that modulates the frequency, rate or extent of potassium ion transmembrane transport.
    GO:2000008    regulation of protein localization to cell surface    Any process that modulates the frequency, rate or extent of protein localization to the cell surface.
    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:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0043679    axon terminus    Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal button is a specialized region of it.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0031234    extrinsic component of cytoplasmic side of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.
    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:0044224    juxtaparanode region of axon    A region of an axon near a node of Ranvier that is between the paranode and internode regions.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:1990031    pinceau fiber    Dense plexus formed by the descending collaterals of cerebellar basket cells that wrap around a Purkinje cell axonal initial segment.
    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:0014069    postsynaptic density of dendrite    An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.
    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.

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(-) Related Entries Specified in the PDB File

1qrq STRUCTURE OF A VOLTAGE-DEPENDENT K+ CHANNEL SUBUNIT