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

(-) Description

Title :  OXIDIZED (CU2+) PEPTIDYLGLYCINE ALPHA-HYDROXYLATING MONOOXYGENASE (PHM) WITH BOUND NITRITE
 
Authors :  E. E. Chufan, B. A. Eipper, R. E. Mains, L. M. Amzel
Date :  10 Apr 10  (Deposition) - 24 Nov 10  (Release) - 24 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Monooxygenase, Bioactive Peptide Activation, Ascorbate (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. E. Chufan, S. T. Prigge, X. Siebert, B. A. Eipper, R. E. Mains, L. M. Amzel
Differential Reactivity Between The Two Copper Sites Of Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm)
J. Am. Chem. Soc. V. 132 15565 2010
PubMed-ID: 20958070  |  Reference-DOI: 10.1021/JA103117R

(-) Compounds

Molecule 1 - PEPTIDYL-GLYCINE ALPHA-AMIDATING MONOOXYGENASE
    ChainsA
    EC Number1.14.17.3
    EngineeredYES
    Expression SystemCRICETULUS GRISEUS
    Expression System PlasmidPCIS
    Expression System StrainCHO DG44
    Expression System Taxid10029
    Expression System Vector TypeVIRUS
    FragmentUNP RESIDUES 43-356, MONOOXYGENASE DOMAIN
    GenePAM
    Organism CommonRAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    StrainSPRAGUE-DAWLEY
    SynonymPAM, PEPTIDYLGLYCINE ALPHA-HYDROXYLATING MONOOXYGENASE, PHM

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
1CU2Ligand/IonCOPPER (II) ION
2GOL3Ligand/IonGLYCEROL
3NI1Ligand/IonNICKEL (II) ION
4NO23Ligand/IonNITRITE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:107 , HIS A:108 , HIS A:172BINDING SITE FOR RESIDUE CU A 357
2AC2SOFTWARENO2 A:1 , HIS A:242 , HIS A:244 , MET A:314BINDING SITE FOR RESIDUE CU A 358
3AC3SOFTWARENO2 A:2 , HIS A:235 , HIS A:305 , HOH A:463 , HOH A:486BINDING SITE FOR RESIDUE NI A 359
4AC4SOFTWAREHIS A:242 , HIS A:244 , GLY A:308 , MET A:314 , CU A:358BINDING SITE FOR RESIDUE NO2 A 1
5AC5SOFTWAREHOH A:40 , HIS A:235 , ASP A:282 , ASP A:312 , NI A:359 , HOH A:463 , HOH A:486BINDING SITE FOR RESIDUE NO2 A 2
6AC6SOFTWAREVAL A:255 , ASN A:257 , GLY A:258 , GLY A:286 , ILE A:288BINDING SITE FOR RESIDUE NO2 A 3
7AC7SOFTWAREHOH A:7 , HOH A:8 , LEU A:138 , TYR A:139 , THR A:148 , MET A:320 , HOH A:378 , HOH A:387BINDING SITE FOR RESIDUE GOL A 360
8AC8SOFTWAREHOH A:23 , ASN A:136 , PHE A:156 , ARG A:157 , GLY A:163 , SER A:164 , SER A:330 , HOH A:363BINDING SITE FOR RESIDUE GOL A 361
9AC9SOFTWARETYR A:205 , GLN A:228 , LYS A:230 , MET A:231 , THR A:333 , HOH A:388BINDING SITE FOR RESIDUE GOL A 362

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:47 -A:186
2A:81 -A:126
3A:114 -A:131
4A:227 -A:334
5A:293 -A:315

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MIB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MIB)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CU2_MONOOXYGENASE_1PS00084 Copper type II, ascorbate-dependent monooxygenases signature 1.AMD_RAT107-114  1A:107-114
2CU2_MONOOXYGENASE_2PS00085 Copper type II, ascorbate-dependent monooxygenases signature 2.AMD_RAT235-247  1A:235-247

(-) Exons   (11, 11)

Asymmetric/Biological Unit (11, 11)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000434511ENSRNOE00000312990chr9:96893071-96893356286AMD_RAT1-35350--
1.2ENSRNOT000000434512ENSRNOE00000111526chr9:96894215-96894335121AMD_RAT35-75411A:45-7531
1.3ENSRNOT000000434513ENSRNOE00000111589chr9:96922951-9692300858AMD_RAT76-95201A:76-9520
1.4ENSRNOT000000434514ENSRNOE00000111641chr9:96933678-9693376588AMD_RAT95-124301A:95-12430
1.5ENSRNOT000000434515ENSRNOE00000111712chr9:96945410-9694549586AMD_RAT124-153301A:124-15330
1.6ENSRNOT000000434516ENSRNOE00000111761chr9:96946758-9694684184AMD_RAT153-181291A:153-17927
1.7ENSRNOT000000434517ENSRNOE00000111838chr9:96973214-9697326249AMD_RAT181-197171A:182-19716
1.8ENSRNOT000000434518ENSRNOE00000111893chr9:96974658-9697472568AMD_RAT197-220241A:197-22024
1.9ENSRNOT000000434519ENSRNOE00000111971chr9:96975839-9697591981AMD_RAT220-247281A:220-24728
1.10ENSRNOT0000004345110ENSRNOE00000112028chr9:96976178-9697625477AMD_RAT247-272261A:247-27226
1.11ENSRNOT0000004345111ENSRNOE00000112095chr9:96977435-96977538104AMD_RAT273-307351A:273-30735
1.13ENSRNOT0000004345113ENSRNOE00000112162chr9:96987329-96987513185AMD_RAT307-369631A:307-35448
1.14ENSRNOT0000004345114ENSRNOE00000245578chr9:96989214-9698928572AMD_RAT369-393250--
1.15aENSRNOT0000004345115aENSRNOE00000314250chr9:97001605-97001919315AMD_RAT393-4981060--
1.16ENSRNOT0000004345116ENSRNOE00000112300chr9:97011332-97011461130AMD_RAT498-541440--
1.18ENSRNOT0000004345118ENSRNOE00000245555chr9:97020681-97020797117AMD_RAT541-580400--
1.19ENSRNOT0000004345119ENSRNOE00000112441chr9:97023054-9702312673AMD_RAT580-604250--
1.20ENSRNOT0000004345120ENSRNOE00000112508chr9:97024339-97024549211AMD_RAT605-675710--
1.21ENSRNOT0000004345121ENSRNOE00000112572chr9:97024746-97024946201AMD_RAT675-742680--
1.22ENSRNOT0000004345122ENSRNOE00000112706chr9:97027717-97027832116AMD_RAT742-780390--
1.23bENSRNOT0000004345123bENSRNOE00000350802chr9:97030939-97031047109AMD_RAT781-817370--
1.24ENSRNOT0000004345124ENSRNOE00000112838chr9:97037983-9703803654AMD_RAT817-835190--
1.25aENSRNOT0000004345125aENSRNOE00000451699chr9:97043264-97043467204AMD_RAT835-903690--
1.26aENSRNOT0000004345126aENSRNOE00000446469chr9:97046192-9704621726AMD_RAT903-91190--
1.27ENSRNOT0000004345127ENSRNOE00000457036chr9:97046321-970463244AMD_RAT912-91320--
1.31aENSRNOT0000004345131aENSRNOE00000344739chr9:97046660-97046865206AMD_RAT913-980680--

(-) 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:308
 aligned with AMD_RAT | P14925 from UniProtKB/Swiss-Prot  Length:976

    Alignment length:310
                                    54        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
              AMD_RAT    45 NECLGTIGPVTPLDASDFALDIRMPGVTPKESDTYFCMSMRLPVDEEAFVIDFKPRASMDTVHHMLLFGCNMPSSTGSYWFCDEGTCTDKANILYAWARNAPPTRLPKGVGFRVGGETGSKYFVLQVHYGDISAFRDNHKDCSGVSVHLTRVPQPLIAGMYLMMSVDTVIPPGEKVVNADISCQYKMYPMHVFAYRVHTHHLGKVVSGYRVRNGQWTLIGRQNPQLPQAFYPVEHPVDVTFGDILAARCVFTGEGRTEATHIGGTSSDEMCNLYIMYYMEAKYALSFMTCTKNVAPDMFRTIPAEANIPI 354
               SCOP domains d3miba1 A:45-198 Peptidylglycine alpha-hydroxylating monooxygenase, PHM                                                                                   d3miba2 A:199-354 Peptidylglycine alpha-hydroxylating monooxygenase, PHM                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------Cu2_monooxygen-3mibA02 A:62-184                                                                                            --------------Cu2_monoox_C-3mibA01 A:199-350                                                                                                                          ---- Pfam domains
         Sec.struct. author ...hhhhh.eee....eeeeeee..........eeeeeeee......eeeeeeeee.....eeeeeeeee.........ee.hhh......eeeeeee...........eeeee.......eeeeeeee......--......eeeeeee.....eeeeeeeee....ee......eeeeeeee.....eeeeeeeee....eeeeeeeeee..eeeeeeee........eeeeeeeee....eeeeeeee........ee..........eeeeeeeee......eeee....hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------CU2_MONO------------------------------------------------------------------------------------------------------------------------CU2_MONOOXYGE----------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:45-75         Exon 1.3            ----------------------------Exon 1.5  PDB: A:124-153      ---------------------------Exon 1.7         -------------------------------------------------Exon 1.10  PDB: A:247-272 Exon 1.11  PDB: A:273-307          ----------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------Exon 1.4  PDB: A:95-124       ----------------------------Exon 1.6  PDB: A:153-179     ---------------Exon 1.8  PDB: A:197-220--------------------------------------------------------------------------------------Exon 1.13  PDB: A:307-354 UniProt: 307-369       Transcript 1 (2)
           Transcript 1 (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: A:220-247    ----------------------------------------------------------------------------------------------------------- Transcript 1 (3)
                 3mib A  45 NECLGTIGPVTPLDASDFALDIRMPGVTPKESDTYFCMSMRLPVDEEAFVIDFKPRASMDTVHHMLLFGCNMPSSTGSYWFCDEGTCTDKANILYAWARNAPPTRLPKGVGFRVGGETGSKYFVLQVHYGDISAF--NHKDCSGVSVHLTRVPQPLIAGMYLMMSVDTVIPPGEKVVNADISCQYKMYPMHVFAYRVHTHHLGKVVSGYRVRNGQWTLIGRQNPQLPQAFYPVEHPVDVTFGDILAARCVFTGEGRTEATHIGGTSSDEMCNLYIMYYMEAKYALSFMTCTKNVAPDMFRTIPAEANIPI 354
                                    54        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
                                                                                                                                                                179  |                                                                                                                                                                            
                                                                                                                                                                   182                                                                                                                                                                            

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MIB)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (54, 54)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AMD_RAT | P14925)
molecular function
    GO:0031418    L-ascorbic acid binding    Interacting selectively and non-covalently with L-ascorbic acid, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate; L-ascorbic acid is vitamin C and has co-factor and anti-oxidant activities in many species.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004497    monooxygenase activity    Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
    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:0016715    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from reduced ascorbate and one other donor, and one atom of oxygen is incorporated into one donor.
    GO:0004598    peptidylamidoglycolate lyase activity    Catalysis of the reaction: peptidylamidoglycolate = peptidyl amide + glyoxylate.
    GO:0004504    peptidylglycine monooxygenase activity    Catalysis of the reaction: peptidyl-glycine + ascorbate + O2 = peptidyl(2-hydroxyglycine) + dehydroascorbate + H2O.
    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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0007417    central nervous system development    The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0007595    lactation    The regulated release of milk from the mammary glands and the period of time that a mother lactates to feed her young.
    GO:0060173    limb development    The process whose specific outcome is the progression of a limb over time, from its formation to the mature structure. A limb is an appendage of an animal used for locomotion or grasping. Examples include legs, arms or some types of fin.
    GO:0001676    long-chain fatty acid metabolic process    The chemical reactions and pathways involving long-chain fatty acids, A long-chain fatty acid is a fatty acid with a chain length between C13 and C22.
    GO:0060135    maternal process involved in female pregnancy    A reproductive process occurring in the mother that allows an embryo or fetus to develop within it.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0042476    odontogenesis    The process whose specific outcome is the progression of a tooth or teeth over time, from formation to the mature structure(s). A tooth is any hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food.
    GO:0022602    ovulation cycle process    A process involved in the sexual cycle seen in females, often with physiologic changes in the endometrium that recur at regular intervals during the reproductive years.
    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:0001519    peptide amidation    The posttranslational conversion of C-terminal glycine-extended peptides to C-terminal alpha-amidated peptides. Occurs to over half of all peptide hormones to give bioactive peptides. This is a two step process catalyzed by a peptidyl-glycine alpha-hydroxylating monooxygenase and a peptidyl-alpha-hydroxyglycine alpha-amidating lyase. In some organisms, this process is catalyzed by two separate enzymes, whereas in higher organisms, one polypeptide catalyzes both reactions.
    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:0018032    protein amidation    Addition of an amide group from a glycine to a protein amino acid.
    GO:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0019538    protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification.
    GO:0032956    regulation of actin cytoskeleton organization    Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0050708    regulation of protein secretion    Any process that modulates the frequency, rate or extent of the controlled release of a protein from a cell.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0046688    response to copper ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a copper ion stimulus.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0032355    response to estradiol    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
    GO:0051384    response to glucocorticoid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
    GO:0001666    response to hypoxia    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0009268    response to pH    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pH stimulus. pH is a measure of the acidity or basicity of an aqueous solution.
    GO:0009404    toxin metabolic process    The chemical reactions and pathways involving a toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    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:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    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:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0043204    perikaryon    The portion of the cell soma (neuronal cell body) that excludes the nucleus.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    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:0030141    secretory granule    A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.
    GO:0030667    secretory granule membrane    The lipid bilayer surrounding a secretory granule.
    GO:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.
    GO:0030658    transport vesicle membrane    The lipid bilayer surrounding a transport vesicle.

 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
    CU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NO2  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3mib)
 

(-) 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
  3mib
    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
  AMD_RAT | P14925
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.14.17.3
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    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
  AMD_RAT | P14925
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        AMD_RAT | P149251opm 1phm 1sdw 1yi9 1yip 1yjk 1yjl 3fvz 3fw0 3mic 3mid 3mie 3mif 3mig 3mih 3mlj 3mlk 3mll 3phm 4e4z

(-) Related Entries Specified in the PDB File

1phm OXIDIZED (CU2+) PHM
3mic OXIDIZED (CU2+) PHM WITH BOUND AZIDE
3mid OXIDIZED (CU2+) PHM WITH BOUND AZIDE OBTAINED BY SOAKING (100MM NAN3)
3mie OXIDIZED (CU2+) PHM WITH BOUND AZIDE OBTAINED BY SOAKING (50MM NAN3)
3mif OXIDIZED (CU2+) PHM WITH BOUND CARBON MONOXIDE
3mig OXIDIZED (CU2+) PHM WITH BOUND NITRITE, OBTAINED IN THE PRESENCE OF SUBSTRATE
3mih OXIDIZED (CU2+) PHM WITH BOUND AZIDE, OBTAINED IN THE PRESENCE OF SUBSTRATE
3mlj REDUCED (CU+) PHM WITH BOUND CO
3mlk REDUCED (CU+) PHM WITH BOUND NITRITE
3mll REDUCED (CU+) PHM WITH BOUND AZIDE