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(-) Description

Title :  CRYSTAL STRUCTURE OF MTMR2 IN COMPLEX WITH PHOSPHATIDYLINOSITOL 3-PHOSPHATE
 
Authors :  M. J. Begley, G. S. Taylor, M. A. Brock, P. Ghosh, V. L. Woods, J. E. Dixon
Date :  25 May 05  (Deposition) - 31 Jan 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.82
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein-Phospholipid Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. J. Begley, G. S. Taylor, M. A. Brock, P. Ghosh, V. L. Woods, J. E. Dixon
Molecular Basis For Substrate Recognition By Mtmr2, A Myotubularin Family Phosphoinositide Phosphatase
Proc. Natl. Acad. Sci. Usa V. 103 927 2006
PubMed-ID: 16410353  |  Reference-DOI: 10.1073/PNAS.0510006103
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MYOTUBULARIN-RELATED PROTEIN 2
    ChainsA
    EC Number3.1.3.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET21A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentPH-GRAM AND PHOSPHATASE DOMAINS
    GeneMTMR2, KIAA1073
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2PIB1Ligand/Ion2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:458 , ARG A:463 , VAL A:464 , SER A:477 , PRO A:478 , VAL A:479 , PHE A:480 , LEU A:481 , LEU A:512 , HOH A:1040BINDING SITE FOR RESIDUE EDO A 1878
2AC2SOFTWAREARG A:360 , ALA A:472 , HOH A:1086 , HOH A:1279BINDING SITE FOR RESIDUE EDO A 1879
3AC3SOFTWARELYS A:156 , TYR A:513 , HOH A:1033 , HOH A:1044 , HOH A:1225 , HOH A:1382BINDING SITE FOR RESIDUE EDO A 1880
4AC4SOFTWAREVAL A:358 , SER A:362 , LYS A:365 , THR A:386 , HIS A:387 , HIS A:391BINDING SITE FOR RESIDUE EDO A 1881
5AC5SOFTWAREASN A:330 , LYS A:333 , ASN A:355 , ILE A:356 , SER A:417 , SER A:418 , ASP A:419 , GLY A:420 , TRP A:421 , ASP A:422 , ARG A:423 , ARG A:463 , GLU A:549 , HOH A:1002 , HOH A:1089 , HOH A:1141 , HOH A:3721 , HOH A:3758BINDING SITE FOR RESIDUE PIB A 3632

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ile A:220 -Pro A:221
2Tyr A:371 -Pro A:372

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_047947R283WMTMR2_HUMANDisease (CMT4B1)  ---AR283W
2UniProtVAR_047256N545SMTMR2_HUMANPolymorphism558018AN545S

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PPASE_MYOTUBULARINPS51339 Myotubularin phosphatase domain.MTMR2_HUMAN205-580  1A:205-580
2TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.MTMR2_HUMAN386-433  1A:386-433
3TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.MTMR2_HUMAN415-425  1A:415-425

(-) Exons   (12, 12)

Asymmetric/Biological Unit (12, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3aENST000003462993aENSE00001894742chr11:95657459-95657039421MTMR2_HUMAN1-27270--
1.7ENST000003462997ENSE00001698940chr11:95621425-95621320106MTMR2_HUMAN27-62360--
1.11cENST0000034629911cENSE00001729203chr11:95598840-9559876576MTMR2_HUMAN63-88261A:73-8816
1.12bENST0000034629912bENSE00001099211chr11:95595530-9559543695MTMR2_HUMAN88-119321A:88-11932
1.13cENST0000034629913cENSE00001099206chr11:95595266-95595156111MTMR2_HUMAN120-156371A:120-15637
1.14ENST0000034629914ENSE00001099217chr11:95591796-95591695102MTMR2_HUMAN157-190341A:157-19034
1.15ENST0000034629915ENSE00001099204chr11:95590799-9559071684MTMR2_HUMAN191-218281A:191-21828
1.16bENST0000034629916bENSE00001099224chr11:95583913-95583764150MTMR2_HUMAN219-268501A:219-26850
1.17ENST0000034629917ENSE00001099221chr11:95583026-95582838189MTMR2_HUMAN269-331631A:269-33163
1.18ENST0000034629918ENSE00001800236chr11:95581063-95580878186MTMR2_HUMAN332-393621A:332-39362
1.19ENST0000034629919ENSE00001099218chr11:95578323-95578117207MTMR2_HUMAN394-462691A:394-46269
1.20ENST0000034629920ENSE00001099223chr11:95574873-9557478193MTMR2_HUMAN463-493311A:463-49331
1.21ENST0000034629921ENSE00001099215chr11:95571371-95571258114MTMR2_HUMAN494-531381A:494-53138
1.22ENST0000034629922ENSE00001099209chr11:95569488-95569312177MTMR2_HUMAN532-590591A:532-58554
1.23dENST0000034629923dENSE00001121601chr11:95568615-955660462570MTMR2_HUMAN591-643530--

(-) 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:513
 aligned with MTMR2_HUMAN | Q13614 from UniProtKB/Swiss-Prot  Length:643

    Alignment length:513
                                    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       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582   
          MTMR2_HUMAN    73 MEEPPLLPGENIKDMAKDVTYICPFTGAVRGTLTVTNYRLYFKSMERDPPFVLDASLGVINRVEKIGGASSRGENSYGLETVCKDIRNLRFAHKPEGRTRRSIFENLMKYAFPVSNNLPLFAFEYKEVFPENGWKLYDPLLEYRRQGIPNESWRITKINERYELCDTYPALLVVPANIPDEELKRVASFRSRGRIPVLSWIHPESQATITRCSQPMVGVSGKRSKEDEKYLQAIMDSNAQSHKIFIFDARPSVNAVANKAKGGGYESEDAYQNAELVFLDIHNIHVMRESLRKLKEIVYPNIEETHWLSNLESTHWLEHIKLILAGALRIADKVESGKTSVVVHCSDGWDRTAQLTSLAMLMLDGYYRTIRGFEVLVEKEWLSFGHRFQLRVGHGDKNHADADRSPVFLQFIDCVWQMTRQFPTAFEFNEYFLITILDHLYSCLFGTFLCNSEQQRGKENLPKRTVSLWSYINSQLEDFTNPLYGSYSNHVLYPVASMRHLELWVGYYIRWNP 585
               SCOP domains d1zsqa1 A:73-198 Myotubularin-related protein 2, N-terminal domain                                                            d1zsqa2 A:199-585 Myotubularin-related protein 2, C-terminal domain                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ----------1zsqA01 A:83-183 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains GRAM-1zsqA01 A:73-139                                              ----------------------------------------------------------------------------------------------Myotub-related-1zsqA03 A:234-351                                                                                      -----------------------------------------------------------Y_phosphatase_m-1zsqA02 A:411-465                      ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eeeeeeeeeeee...eeeeeeeeee..eeeeee......eeeeee...eeeeeee...........eeeeee...eeeeee.hhhhhhhhhhhhhhhhhh........hhhhh.......hhhhh.hhhhhhhhh......eeee...............eeee...hhhhhhhhhhhhhhhh..eeeee......eeeee...........hhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhh...........eeeee....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh............hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.hhhhhhhhhhhhhh.......................hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------W---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S---------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------------------------------------------------------------------------------------PPASE_MYOTUBULARIN  PDB: A:205-580 UniProt: 205-580                                                                                                                                                                                                                                                                                                                                     ----- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:386-433               -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
           Transcript 1 (1) Exon 1.11c      -------------------------------Exon 1.13c  PDB: A:120-156           Exon 1.14  PDB: A:157-190         Exon 1.15  PDB: A:191-218   Exon 1.16b  PDB: A:219-268 UniProt: 219-268       Exon 1.17  PDB: A:269-331 UniProt: 269-331                     Exon 1.18  PDB: A:332-393 UniProt: 332-393                    Exon 1.19  PDB: A:394-462 UniProt: 394-462                           Exon 1.20  PDB: A:463-493      Exon 1.21  PDB: A:494-531             Exon 1.22  PDB: A:532-585 UniProt: 532-590             Transcript 1 (1)
           Transcript 1 (2) ---------------Exon 1.12b  PDB: A:88-119       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1zsq A  73 MEEPPLLPGENIKDMAKDVTYICPFTGAVRGTLTVTNYRLYFKSMERDPPFVLDASLGVINRVEKIGGASSRGENSYGLETVCKDIRNLRFAHKPEGRTRRSIFENLMKYAFPVSNNLPLFAFEYKEVFPENGWKLYDPLLEYRRQGIPNESWRITKINERYELCDTYPALLVVPANIPDEELKRVASFRSRGRIPVLSWIHPESQATITRCSQPMVGVSGKRSKEDEKYLQAIMDSNAQSHKIFIFDARPSVNAVANKAKGGGYESEDAYQNAELVFLDIHNIHVMRESLRKLKEIVYPNIEETHWLSNLESTHWLEHIKLILAGALRIADKVESGKTSVVVHSSDGWDRTAQLTSLAMLMLDGYYRTIRGFEVLVEKEWLSFGHRFQLRVGHGDKNHADADRSPVFLQFIDCVWQMTRQFPTAFEFNEYFLITILDHLYSCLFGTFLCNSEQQRGKENLPKRTVSLWSYINSQLEDFTNPLYGSYSNHVLYPVASMRHLELWVGYYIRWNP 585
                                    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       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582   

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: PH (111)

(-) Gene Ontology  (40, 40)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MTMR2_HUMAN | Q13614)
molecular function
    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:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0052866    phosphatidylinositol phosphate phosphatase activity    Catalysis of the reaction: phosphatidylinositol phosphate(n) + H2O = phosphatidylinositol phosphate(n-1) + phosphate. This reaction is the removal of a phosphate group from a phosphatidylinositol phosphate.
    GO:0052629    phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity    Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate + H2O = a 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate + 2 H+.
    GO:0004438    phosphatidylinositol-3-phosphatase activity    Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 3-phosphate + H2O = 1-phosphatidyl-1D-myo-inositol + phosphate.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0004725    protein tyrosine phosphatase activity    Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
    GO:0008138    protein tyrosine/serine/threonine phosphatase activity    Catalysis of the reactions: protein serine + H2O = protein serine + phosphate; protein threonine phosphate + H2O = protein threonine + phosphate; and protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
biological process
    GO:0097062    dendritic spine maintenance    The organization process that preserves a dendritic spine in a stable functional or structural state. A dendritic spine is a specialized protrusion from a neuronal dendrite and is involved in synaptic transmission.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0046855    inositol phosphate dephosphorylation    The process of removing a phosphate group from any mono- or polyphosphorylated inositol.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0032288    myelin assembly    The process in which the wraps of cell membrane that constitute myelin are laid down around an axon in the central or peripheral nervous system.
    GO:0045806    negative regulation of endocytosis    Any process that stops, prevents, or reduces the frequency, rate or extent of endocytosis.
    GO:0090394    negative regulation of excitatory postsynaptic potential    Any process that prevents the establishment or decreases the extent of the excitatory postsynaptic potential (EPSP) which is a temporary increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential.
    GO:0031642    negative regulation of myelination    Any process that stops, prevents, or reduces the frequency, rate or extent of the formation of a myelin sheath around nerve axons.
    GO:2000645    negative regulation of receptor catabolic process    Any process that stops, prevents or reduces the frequency, rate or extent of receptor catabolic process.
    GO:0002091    negative regulation of receptor internalization    Any process that stops, prevents, or reduces the frequency, rate or extent of receptor internalization.
    GO:0048666    neuron development    The process whose specific outcome is the progression of a neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
    GO:0035335    peptidyl-tyrosine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
    GO:0006661    phosphatidylinositol biosynthetic process    The chemical reactions and pathways resulting in the formation of phosphatidylinositol, any glycophospholipid in which the sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
    GO:0046856    phosphatidylinositol dephosphorylation    The process of removing one or more phosphate groups from a phosphatidylinositol.
    GO:0046488    phosphatidylinositol metabolic process    The chemical reactions and pathways involving phosphatidylinositol, any glycophospholipid in which a sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
    GO:2000643    positive regulation of early endosome to late endosome transport    Any process that activates or increases the frequency, rate or extent of early endosome to late endosome transport.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:0051262    protein tetramerization    The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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:0043197    dendritic spine    A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.
    GO:0031901    early endosome membrane    The lipid bilayer surrounding an early endosome.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0097060    synaptic membrane    A specialized area of membrane on either the presynaptic or the postsynaptic side of a synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell.
    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.
    GO:0005774    vacuolar membrane    The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MTMR2_HUMAN | Q136141lw3 1m7r 1zvr

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1ZSQ)