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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN MONO-GLYCERIDE LIPASE
 
Authors :  T. Bertrand, F. Auge, J. Houtmann, A. Rak, F. Vallee, V. Mikol, P. F. Bern N. Michot, D. Cheuret, C. Hoornaert, M. Mathieu
Date :  18 Sep 09  (Deposition) - 26 Jan 10  (Release) - 11 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A  (4x)
Biol. Unit 4:  B  (4x)
Keywords :  Alpha-Beta Hydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Bertrand, F. Auge, J. Houtmann, A. Rak, F. Vallee, V. Mikol, P. F. Berne, N. Michot, D. Cheuret, C. Hoornaert, M. Mathieu
Structural Basis For Human Monoglyceride Lipase Inhibition.
J. Mol. Biol. V. 396 663 2010
PubMed-ID: 19962385  |  Reference-DOI: 10.1016/J.JMB.2009.11.060

(-) Compounds

Molecule 1 - MGLL PROTEIN
    ChainsA, B
    EC Number3.1.1.23
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    GeneMGLL, HCG_40840
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMONOGLYCERIDE LIPASE, ISOFORM CRA_B, CDNA, FLJ96595, HOMO SAPIENS MONOGLYCERIDE LIPASE (MGLL), MRNA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (4x)A 
Biological Unit 4 (4x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 23)

Asymmetric Unit (3, 23)
No.NameCountTypeFull Name
1MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MRD5Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
3MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MRD3Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
3MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (3, 11)
No.NameCountTypeFull Name
1MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MRD2Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
3MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (3, 48)
No.NameCountTypeFull Name
1MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MRD12Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
3MSE32Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (3, 44)
No.NameCountTypeFull Name
1MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MRD8Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
3MSE32Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:158 , ALA A:161 , ASN A:162 , SER A:165 , ALA A:166 , GLY A:220 , MRD A:831 , MRD A:886BINDING SITE FOR RESIDUE MPD A 707
2AC2SOFTWARESER A:132 , HOH A:445 , HOH A:513 , MPD A:707BINDING SITE FOR RESIDUE MRD A 831
3AC3SOFTWAREALA A:61 , HIS A:131 , ILE A:189 , LEU A:251 , HIS A:279 , VAL A:280 , HOH A:445 , HOH A:529BINDING SITE FOR RESIDUE MRD A 866
4AC4SOFTWARESER A:165 , LYS A:170 , LEU A:186 , MPD A:707BINDING SITE FOR RESIDUE MRD A 886
5AC5SOFTWAREALA B:161 , ASN B:162 , SER B:165 , LEU B:215 , LEU B:223 , HOH B:456 , MRD B:830BINDING SITE FOR RESIDUE MPD B 812
6AC6SOFTWARESER B:132 , HOH B:444 , HOH B:516 , MPD B:812BINDING SITE FOR RESIDUE MRD B 830
7AC7SOFTWAREGLY B:60 , ALA B:61 , GLU B:63 , HIS B:131 , LEU B:194 , TYR B:204 , LEU B:251 , HIS B:279 , VAL B:280 , HOH B:444 , HOH B:447 , HOH B:516BINDING SITE FOR RESIDUE MRD B 865

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3JW8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3JW8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3JW8)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPASE_SERPS00120 Lipases, serine active site.MGLL_HUMAN116-125
 
  2A:126-135
B:126-135
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPASE_SERPS00120 Lipases, serine active site.MGLL_HUMAN116-125
 
  1A:126-135
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPASE_SERPS00120 Lipases, serine active site.MGLL_HUMAN116-125
 
  1-
B:126-135
Biological Unit 3 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPASE_SERPS00120 Lipases, serine active site.MGLL_HUMAN116-125
 
  4A:126-135
-
Biological Unit 4 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPASE_SERPS00120 Lipases, serine active site.MGLL_HUMAN116-125
 
  4-
B:126-135

(-) Exons   (0, 0)

(no "Exon" information available for 3JW8)

(-) 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:290
 aligned with MGLL_HUMAN | Q99685 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:290
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295
           MGLL_HUMAN     6 SPRRTPQSIPYQDLPHLVNADGQYLFCRYWKPTGTPKALIFVSHGAGEHSGRYEELARMLMGLDLLVFAHDHVGHGQSEGERMVVSDFHVFVRDVLQHVDSMQKDYPGLPVFLLGHSMGGAIAILTAAERPGHFAGMVLISPLVLANPESATTFKVLAAKVLNLVLPNLSLGPIDSSVLSRNKTEVDIYNSDPLICRAGLKVCFGIQLLNAVSRVERALPKLTVPFLLLQGSADRLCDSKGAYLLMELAKSQDKTLKIYEGAYHVLHKELPEVTNSVFHEINMWVSQRTA 295
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh.eee.....eeeeeee.......eeeeee.....hhhhhhhhhhhhhhh.eeeeee.................hhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhh.....eeeee...........hhhhhhhhhhhhhhh........hhhhh..hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------LIPASE_SER-------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jw8 A  16 SPRRTPQSIPYQDLPHLVNADGQYLFCRYWKPTGTPKALIFVSHGAGEHSGRYEELARmLmGLDLLVFAHDHVGHGQSEGERmVVSDFHVFVRDVLQHVDSmQKDYPGLPVFLLGHSmGGAIAILTAAERPGHFAGmVLISPLVLANPESATTFKVLAAKVLNLVLPNLSLGPIDSSVLSRNKTEVDIYNSDPLICRAGLKVCFGIQLLNAVSRVERALPKLTVPFLLLQGSADRLCDSKGAYLLmELAKSQDKTLKIYEGAYHVLHKELPEVTNSVFHEINmWVSQRTA 305
                                    25        35        45        55        65        75|       85        95  |    105       115 |     125       135       145      |155       165       175       185       195       205       215       225       235       245       255     | 265       275       285       295  |    305
                                                                                     74-MSE                  98-MSE            117-MSE         133-MSE            152-MSE                                                                                                      261-MSE                              298-MSE   
                                                                                       76-MSE                                                                                                                                                                                                                                 

Chain B from PDB  Type:PROTEIN  Length:278
 aligned with MGLL_HUMAN | Q99685 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:278
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287        
           MGLL_HUMAN    18 DLPHLVNADGQYLFCRYWKPTGTPKALIFVSHGAGEHSGRYEELARMLMGLDLLVFAHDHVGHGQSEGERMVVSDFHVFVRDVLQHVDSMQKDYPGLPVFLLGHSMGGAIAILTAAERPGHFAGMVLISPLVLANPESATTFKVLAAKVLNLVLPNLSLGPIDSSVLSRNKTEVDIYNSDPLICRAGLKVCFGIQLLNAVSRVERALPKLTVPFLLLQGSADRLCDSKGAYLLMELAKSQDKTLKIYEGAYHVLHKELPEVTNSVFHEINMWVSQRTA 295
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------Abhydrolase_6-3jw8B01 B:54-292                                                                                                                                                                                                                 ------------- Pfam domains (1)
           Pfam domains (2) --------------------------Abhydrolase_6-3jw8B02 B:54-292                                                                                                                                                                                                                 ------------- Pfam domains (2)
         Sec.struct. author ...eee.....eeeeeee.......eeeeee.....hhhhhhhhhhhhhh..eeeeee.................hhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhh.....eeeee...........hhhhhhhhhhhhhhh........hhhhh..hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------LIPASE_SER-------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jw8 B  28 DLPHLVNADGQYLFCRYWKPTGTPKALIFVSHGAGEHSGRYEELARmLmGLDLLVFAHDHVGHGQSEGERmVVSDFHVFVRDVLQHVDSmQKDYPGLPVFLLGHSmGGAIAILTAAERPGHFAGmVLISPLVLANPESATTFKVLAAKVLNLVLPNLSLGPIDSSVLSRNKTEVDIYNSDPLICRAGLKVCFGIQLLNAVSRVERALPKLTVPFLLLQGSADRLCDSKGAYLLmELAKSQDKTLKIYEGAYHVLHKELPEVTNSVFHEINmWVSQRTA 305
                                    37        47        57        67      | 77        87        97|      107       117       127     | 137       147    |  157       167       177       187       197       207       217       227       237       247       257   |   267       277       287       297|       
                                                                         74-MSE                  98-MSE            117-MSE         133-MSE            152-MSE                                                                                                      261-MSE                              298-MSE   
                                                                           76-MSE                                                                                                                                                                                                                                 

   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  (0, 0)

(no "SCOP Domain" information available for 3JW8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3JW8)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MGLL_HUMAN | Q99685)
molecular function
    GO:0047372    acylglycerol lipase activity    Catalysis of the reaction: H2O + acylglycerol = a fatty acid + glycerol.
    GO:0052689    carboxylic ester hydrolase activity    Catalysis of the hydrolysis of a carboxylic ester bond.
    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:0004622    lysophospholipase activity    Catalysis of the reaction: 2-lysophosphatidylcholine + H2O = glycerophosphocholine + a carboxylate.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0036155    acylglycerol acyl-chain remodeling    Remodeling the acyl chains of an acylglycerol, through sequential deacylation and re-acylation reactions, to generate an acylglycerol containing different types of fatty acid acyl chains.
    GO:0046464    acylglycerol catabolic process    The chemical reactions and pathways resulting in the breakdown of acylglycerol, any mono-, di- or triester of glycerol with (one or more) fatty acids.
    GO:0019369    arachidonic acid metabolic process    The chemical reactions and pathways involving arachidonic acid, a straight chain fatty acid with 20 carbon atoms and four double bonds per molecule. Arachidonic acid is the all-Z-(5,8,11,14)-isomer.
    GO:0006633    fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
    GO:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0016042    lipid catabolic process    The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    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:2000124    regulation of endocannabinoid signaling pathway    Any process that modulates the frequency, rate or extent of endocannabinoid signaling pathway.
    GO:0050727    regulation of inflammatory response    Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.
    GO:0051930    regulation of sensory perception of pain    Any process that modulates the frequency, rate or extent of the 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.
    GO:0009966    regulation of signal transduction    Any process that modulates the frequency, rate or extent of signal transduction.
    GO:0019433    triglyceride catabolic process    The chemical reactions and pathways resulting in the breakdown of a triglyceride, any triester of glycerol.
cellular component
    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:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0019898    extrinsic component of membrane    The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MGLL_HUMAN | Q996853hju 3jwe 3pe6 4uuq

(-) Related Entries Specified in the PDB File

3jwe