Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN NEP COMPLEXED WITH AN IMIDAZO[4,5-C]PYRIDINE INHIBITOR
 
Authors :  S. Sahli, B. Frank, W. B. Schweizer, F. Diederich, D. Blum-Kaelin, J. D. H. J. Bohm, C. Oefner, G. E. Dale
Date :  13 Dec 04  (Deposition) - 07 Jun 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A
Keywords :  Lt1_6, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Sahli, B. Frank, W. B. Schweizer, F. Diederich, D. Blum-Kaelin, J. D. Aebi, H. J. Bohm, C. Oefner, G. E. Dale
Second-Generation Inhibitors For The Metalloprotease Neprilysin Based On Bicyclic Heteroaromatic Scaffolds: Synthesis, Biological Activity, And X-Ray Crystal Structure Analysis
Helv. Chim. Acta V. 88 731 2005
PubMed: search  |  Reference-DOI: 10.1002/HLCA.200590051

(-) Compounds

Molecule 1 - NEPRILYSIN
    ChainsA
    EC Number3.4.24.11
    EngineeredYES
    Expression SystemSACCHAROMYCES CEREVISIAE
    Expression System CommonBAKER'S YEAST
    Expression System Taxid4932
    FragmentEXTRACELLULAR DOMAIN (RESIDUES 54-179)
    GeneMME, EPN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNEUTRAL ENDOPEPTIDASE, NEP, ENKEPHALINASE, COMMON ACUTE LYMPHOCYTIC LEUKEMIA ANTIGEN, CALLA, NEUTRAL ENDOPEPTIDASE 24.11, CD10

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
3STS1Ligand/Ion2-[(1S)-1-BENZYL-2-SULFANYLETHYL]-1H-IMIDAZO[4,5-C]PYRIDIN-5-IUM
4ZN1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:144 , ALA A:147BINDING SITE FOR RESIDUE NAG A 752
2AC2SOFTWAREASN A:324 , ASN A:327 , GLU A:328 , HOH A:1046 , HOH A:1047BINDING SITE FOR RESIDUE NAG A 753
3AC3SOFTWARETYR A:623 , GLY A:626 , ASN A:627BINDING SITE FOR RESIDUE NAG A 754
4AC4SOFTWAREHIS A:583 , HIS A:587 , GLU A:646 , STS A:900BINDING SITE FOR RESIDUE ZN A 800
5AC5SOFTWAREVAL A:198 , LEU A:199 , ARG A:222 , LEU A:223 , GLU A:279 , ILE A:282 , ARG A:373BINDING SITE FOR RESIDUE ACT A 801
6AC6SOFTWAREARG A:110 , ASN A:542 , ALA A:543 , MET A:579 , HIS A:583 , GLU A:584 , GLU A:646 , TRP A:693 , HIS A:711 , ARG A:717 , ZN A:800BINDING SITE FOR RESIDUE STS A 900

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:56 -A:61
2A:79 -A:734
3A:87 -A:694
4A:142 -A:410
5A:233 -A:241
6A:620 -A:746

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:318 -Pro A:319
2Pro A:561 -Pro A:562

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 6)

Asymmetric/Biological Unit (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_077685C143YNEP_HUMANDisease (SCA43)879255651AC142Y
2UniProtVAR_077686Y347CNEP_HUMANDisease (CMT2T)138218277AY346C
3UniProtVAR_077687A348PNEP_HUMANUnclassified (CMT2T)199567914AA347P
4UniProtVAR_077689A422DNEP_HUMANDisease (CMT2T)777476150AA421D
5UniProtVAR_077690Y497HNEP_HUMANPolymorphism200308207AY496H
6UniProtVAR_077691C621RNEP_HUMANDisease (CMT2T)879253752AC620R

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.NEP_HUMAN581-590  1A:580-589

(-) Exons   (21, 21)

Asymmetric/Biological Unit (21, 21)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.4dENST000003604904dENSE00001513376chr3:154798188-15479825568NEP_HUMAN-00--
1.9bENST000003604909bENSE00002152527chr3:154801947-154802116170NEP_HUMAN1-54540--
1.10aENST0000036049010aENSE00001019489chr3:154802848-15480288336NEP_HUMAN54-66131A:54-6512
1.13cENST0000036049013cENSE00002199839chr3:154832783-154832944162NEP_HUMAN66-120551A:65-11955
1.14ENST0000036049014ENSE00000934032chr3:154834268-15483434881NEP_HUMAN120-147281A:119-14628
1.15bENST0000036049015bENSE00000934033chr3:154834453-15483454896NEP_HUMAN147-179331A:146-17833
1.16ENST0000036049016ENSE00000934034chr3:154834657-154834775119NEP_HUMAN179-218401A:178-21740
1.17bENST0000036049017bENSE00000934035chr3:154836535-15483660066NEP_HUMAN219-240221A:218-23922
1.18ENST0000036049018ENSE00001019488chr3:154855891-154856025135NEP_HUMAN241-285451A:240-28445
1.19ENST0000036049019ENSE00000934036chr3:154857980-154858081102NEP_HUMAN286-319341A:285-31834
1.20ENST0000036049020ENSE00000934037chr3:154859780-154859916137NEP_HUMAN320-365461A:319-36446
1.21ENST0000036049021ENSE00000934038chr3:154860026-15486011994NEP_HUMAN365-396321A:364-39532
1.22ENST0000036049022ENSE00000934039chr3:154861232-154861360129NEP_HUMAN397-439431A:396-43843
1.23ENST0000036049023ENSE00000934040chr3:154862148-15486224699NEP_HUMAN440-472331A:439-47133
1.24ENST0000036049024ENSE00000934041chr3:154864933-15486501381NEP_HUMAN473-499271A:472-49827
1.25ENST0000036049025ENSE00000779819chr3:154866339-154866442104NEP_HUMAN500-534351A:499-53335
1.26ENST0000036049026ENSE00000779818chr3:154878179-15487823759NEP_HUMAN534-554211A:533-55321
1.27ENST0000036049027ENSE00000779817chr3:154884691-154884810120NEP_HUMAN554-594411A:553-59341
1.28ENST0000036049028ENSE00000779816chr3:154886281-154886414134NEP_HUMAN594-638451A:593-63745
1.29aENST0000036049029aENSE00000779815chr3:154886521-15488658666NEP_HUMAN639-660221A:638-65922
1.30bENST0000036049030bENSE00000779814chr3:154889906-15489000196NEP_HUMAN661-692321A:660-69132
1.31ENST0000036049031ENSE00000779812chr3:154890325-15489040177NEP_HUMAN693-718261A:692-71726
1.32aENST0000036049032aENSE00001182656chr3:154898149-154898277129NEP_HUMAN718-750331A:717-74933

(-) Sequences/Alignments

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:696
 aligned with NEP_HUMAN | P08473 from UniProtKB/Swiss-Prot  Length:750

    Alignment length:696
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744      
            NEP_HUMAN    55 GICKSSDCIKSAARLIQNMDATTEPCTDFFKYACGGWLKRNVIPETSSRYGNFDILRDELEVVLKDVLQEPKTEDIVAVQKAKALYRSCINESAIDSRGGEPLLKLLPDIYGWPVATENWEQKYGASWTAEKAIAQLNSKYGKKVLINLFVGTDDKNSVNHVIHIDQPRLGLPSRDYYECTGIYKEACTAYVDFMISVARLIRQEERLPIDENQLALEMNKVMELEKEIANATAKPEDRNDPMLLYNKMTLAQIQNNFSLEINGKPFSWLNFTNEIMSTVNISITNEEDVVVYAPEYLTKLKPILTKYSARDLQNLMSWRFIMDLVSSLSRTYKESRNAFRKALYGTTSETATWRRCANYVNGNMENAVGRLYVEAAFAGESKHVVEDLIAQIREVFIQTLDDLTWMDAETKKRAEEKALAIKERIGYPDDIVSNDNKLNNEYLELNYKEDEYFENIIQNLKFSQSKQLKKLREKVDKDEWISGAAVVNAFYSSGRNQIVFPAGILQPPFFSAQQSNSLNYGGIGMVIGHEITHGFDDNGRNFNKDGDLVDWWTQQSASNFKEQSQCMVYQYGNFSWDLAGGQHLNGINTLGENIADNGGLGQAYRAYQNYIKKNGEEKLLPGLDLNHKQLFFLNFAQVWCGTYRPEYAVNSIKTDVHSPGNFRIIGTLQNSAEFSEAFHCRKNSYMNPEKKCRVW 750
               SCOP domains d1y8ja_ A: Neutral endopeptidase (neprilysin)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1y8jA01 A:54-103,A:431-482,A:530-749              1y8jA02 A:104-430,A:483-529 Neutral endopeptidase , domain2                                                                                                                                                                                                                                                                            1y8jA01 A:54-103,A:431-482,A:530-749                1y8jA02 A:104-430,A:483-529                    1y8jA01 A:54-103,A:431-482,A:530-749 Collagenase (Catalytic Domain)                                                                                                                                                          CATH domains
               Pfam domains -------------------------Peptidase_M13_N-1y8jA02 A:79-482                                                                                                                                                                                                                                                                                                                                                                                    -----------------------------------------------------------Peptidase_M13-1y8jA01 A:542-748                                                                                                                                                                                - Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.......eeehhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.hhhhh.hhhhhh....hhhhhhhhhhhhh......eeeeeee..eeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhheeeehhhhhhhh.........hhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh....................eee....eeeee.hhh.........hhhhhhhhhhhhhhhhhhhhhh.hhhhh..........hhhhhhhhhhhhhhhhhhhhh..hhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh..eeehhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------Y-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CP-------------------------------------------------------------------------D--------------------------------------------------------------------------H---------------------------------------------------------------------------------------------------------------------------R--------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.10a  -----------------------------------------------------Exon 1.14  PDB: A:119-146   -------------------------------Exon 1.16  PDB: A:178-217               Exon 1.17b            Exon 1.18  PDB: A:240-284 UniProt: 241-285   Exon 1.19  PDB: A:285-318         Exon 1.20  PDB: A:319-364 UniProt: 320-365    -------------------------------Exon 1.22  PDB: A:396-438 UniProt: 397-439 Exon 1.23  PDB: A:439-471        Exon 1.24  PDB: A:472-498  Exon 1.25  PDB: A:499-533          -------------------Exon 1.27  PDB: A:553-593                --------------------------------------------Exon 1.29a            Exon 1.30b  PDB: A:660-691      Exon 1.31  PDB: A:692-717 -------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.13c  PDB: A:65-119 UniProt: 66-120              --------------------------Exon 1.15b  PDB: A:146-178       -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.21  PDB: A:364-395       -----------------------------------------------------------------------------------------------------------------------------------------Exon 1.26            ---------------------------------------Exon 1.28  PDB: A:593-637 UniProt: 594-638   -------------------------------------------------------------------------------Exon 1.32a  PDB: A:717-749        Transcript 1 (2)
                 1y8j A  54 GICKSSDCIKSAARLIQNMDATTEPCTDFFKYACGGWLKRNVIPETSSRYGNFDILRDELEVVLKDVLQEPKTEDIVAVQKAKALYRSCINESAIDSRGGEPLLKLLPDIYGWPVATENWEQKYGASWTAEKAIAQLNSKYGKKVLINLFVGTDDKNSVNHVIHIDQPRLGLPSRDYYECTGIYKEACTAYVDFMISVARLIRQEERLPIDENQLALEMNKVMELEKEIANATAKPEDRNDPMLLYNKMTLAQIQNNFSLEINGKPFSWLNFTNEIMSTVNISITNEEDVVVYAPEYLTKLKPILTKYSARDLQNLMSWRFIMDLVSSLSRTYKESRNAFRKALYGTTSETATWRRCANYVNGNMENAVGRLYVEAAFAGESKHVVEDLIAQIREVFIQTLDDLTWMDAETKKRAEEKALAIKERIGYPDDIVSNDNKLNNEYLELNYKEDEYFENIIQNLKFSQSKQLKKLREKVDKDEWISGAAVVNAFYSSGRNQIVFPAGILQPPFFSAQQSNSLNYGGIGMVIGHEITHGFDDNGRNFNKDGDLVDWWTQQSASNFKEQSQCMVYQYGNFSWDLAGGQHLNGINTLGENIADNGGLGQAYRAYQNYIKKNGEEKLLPGLDLNHKQLFFLNFAQVWCGTYRPEYAVNSIKTDVHSPGNFRIIGTLQNSAEFSEAFHCRKNSYMNPEKKCRVW 749
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743      

   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/Biological Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NEP_HUMAN | P08473)
molecular function
    GO:0004175    endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
    GO:0008238    exopeptidase activity    Catalysis of the hydrolysis of a peptide bond not more than three residues from the N- or C-terminus of a polypeptide chain, in a reaction that requires a free N-terminal amino group, C-terminal carboxyl group or both.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004222    metalloendopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0042277    peptide binding    Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0050435    amyloid-beta metabolic process    The chemical reactions and pathways involving amyloid-beta, a glycoprotein associated with Alzheimer's disease, and its precursor, amyloid precursor protein (APP).
    GO:0002003    angiotensin maturation    The process leading to the attainment of the full functional capacity of angiotensin by conversion of renin substrate into mature angiotensin in the blood.
    GO:0071492    cellular response to UV-A    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a UV-A radiation stimulus. UV-A radiation (UV-A light) spans the wavelengths 315 to 400 nm.
    GO:0071493    cellular response to UV-B    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a UV-B radiation stimulus. UV-B radiation (UV-B light) spans the wavelengths 280 to 315 nm.
    GO:0071345    cellular response to cytokine stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus.
    GO:0046449    creatinine metabolic process    The chemical reactions and pathways involving creatinine, 2-amino-1,5-dihydro-1-methyl-4H-imidazol-4-one, an end product of creatine metabolism and a normal constituent of urine.
    GO:0001822    kidney development    The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine.
    GO:0006518    peptide metabolic process    The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0090399    replicative senescence    A cell aging process associated with the dismantling of a cell as a response to telomere shortening and/or cellular aging.
    GO:0019233    sensory perception of pain    The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process.
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:0005903    brush border    The dense covering of microvilli on the apical surface of a epithelial cells in tissues such as the intestine, kidney, and choroid plexus; the microvilli aid absorption by increasing the surface area of the cell.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    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:0005887    integral component of plasma membrane    The component of the plasma 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:0044306    neuron projection terminus    The specialized, terminal region of a neuron projection such as an axon or a dendrite.
    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: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:0008021    synaptic vesicle    A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    STS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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
    Lys A:318 - Pro A:319   [ RasMol ]  
    Pro A:561 - Pro A:562   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1y8j
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  NEP_HUMAN | P08473
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.24.11
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  617017
    Disease InformationOMIM
  617018
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  NEP_HUMAN | P08473
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        NEP_HUMAN | P084731dl9 1dmt 1qvd 1r1h 1r1i 1r1j 2qpj 2yb9 4cth 5jmy

(-) Related Entries Specified in the PDB File

1dmt 1r1h 1r1i 1r1j