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

(-) Description

Title :  THEORETICAL MODEL OF AN EVMBL8 COMPLEXED WITH THE CEFOTAXIME
 
Authors :  J. K. Lee, T. Moon, H. -S. Park, H. -S. Kim, C. N. Yoon
Date :  25 Nov 05  (Deposition) - 28 Feb 06  (Release) - 02 May 06  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,_#
#:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Metallo Beta-Lactamase, Evmbl8-Cefotaxime Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. -S. Park, S. -H. Nam, J. K. Lee, C. N. Yoon, B. Mannervik, S. J. Benkovic, H. -S. Kim
Design And Evolution Of New Catalytic Activity With An Existing Protein Scaffold.
Science V. 311 535 2006
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METALLO BETA-LACTAMASE
    ChainsA
    EC Number3.5.2.6
    FragmentEVMBL8
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS

 Structural Features

(-) Chains, Units

  
Theoretical Model 
#:   chains that contain no standard or modified protein/DNA/RNA residue)
 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Theoretical Model (2, 3)
No.NameCountTypeFull Name
1CE31Ligand/Ion(6S,7S)-3-[(ACETYLOXY)METHYL]-7-{[(2E)-2-(2-AMINO-1,3-THIAZOL-4-YL)-2-(METHOXYIMINO)ETHANOYL]AMINO}-8-OXO-5-THIA-1-AZABICYCLO[4.2.0]OCT-2-ENE-2-CARBOXYLIC ACID
2ZN2Ligand/IonZINC ION

(-) Sites  (0, 0)

(no "Site" information available for 2F50)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2F50)

(-) Cis Peptide Bonds  (1, 1)

Theoretical Model
No.Residues
1Gly A:29 -Thr A:30

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2F50)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2F50)

(-) Exons   (7, 7)

Theoretical Model (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003973561aENSE00001908102chr16:1877162-1876713450GLO2_HUMAN1-26261A:2-1615
1.3ENST000003973563ENSE00001791655chr16:1873038-1872866173GLO2_HUMAN26-83581A:16-47 (gaps)62
1.4ENST000003973564ENSE00000945924chr16:1872365-187230165GLO2_HUMAN84-105221A:48-6922
1.5ENST000003973565ENSE00000683285chr16:1870015-1869898118GLO2_HUMAN105-144401A:69-11648
1.6ENST000003973566ENSE00000683283chr16:1869224-1869116109GLO2_HUMAN145-181371A:117-15438
1.7ENST000003973567ENSE00001670106chr16:1867272-1867169104GLO2_HUMAN181-215351A:154-18835
1.8ENST000003973568ENSE00001739735chr16:1866995-1866894102GLO2_HUMAN216-249341A:189-1968
1.9ENST000003973569ENSE00001710138chr16:1859834-185975580GLO2_HUMAN250-276270--
1.10bENST0000039735610bENSE00001849129chr16:1859383-1859104280GLO2_HUMAN276-308330--

(-) Sequences/Alignments

Theoretical Model
   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:195
 aligned with GLO2_HUMAN | Q16775 from UniProtKB/Swiss-Prot  Length:308

    Alignment length:225
                                                                                                                                                                                    153                                                                      
                                                                                             78   79                                                 131      132                 152 |                                                                      
                                    21        31        41        51        61        71      |  - |      87        97       107       117       127   |     -  |    139       149  | |  158       168       178       188       198       208       218     
           GLO2_HUMAN    12 SLAALGAACARRGLGPALLGVFCHTDLRKNLTVDEGTMKVEVLPALTDNYMYLVIDDETKEAAIVDP----VQPQKVVDAARKHGVKLTTVLTTHHHWDHAGGNEKLVKLESGLKVYGGDDRIG--------ALTHKITHLSTLQVGSLNVKC-LATPCHTSGHICYFVSKPGGSEPPAVFTGDTLFVAGCGKFYEGTADEMCKALLEVLGRLPPDTRVYCGHEY 223
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....ee...e-------------------------e..-----...eee.......eeee....hhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhh.......eeeeehhhhhhhhhh......eee....eeee..eeee...........................eeee..............hhhhhhhhhhhhhhhh.....eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a      -------------------------------------------------------------Exon 1.4  PDB: A:48-69-----------------------------------------------Exon 1.6  PDB: A:117-154              ----------------------------------Exon 1.8 Transcript 1 (1)
           Transcript 1 (2) --------------Exon 1.3  PDB: A:16-47 (gaps) UniProt: 26-83                  ---------------------Exon 1.5  PDB: A:69-116 UniProt: 105-144        -------------------------------------Exon 1.7  PDB: A:154-188           -------- Transcript 1 (2)
                 2f50 A   2 KVEVLPALTTVAGWG-------------------------EVP-----SNGYLVIDDGTKEAAIVDTPFTAIDTEKLADAAGKHGVEPTTVSATHWHWDCDGGNEELVKLESGPEVYGGDGRINLAKEKWLRALAHKIAHLSTLLVESLSVKCPYPGPGHSTDDICYFASKPGGPEPHPVFRGCFIKPCALPEVLDPTADEMAKALLEVLGRLPLDTRVYYGHEY 196
                                    11    |    -         -         -| |     21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191     
                                         16                        17 |    20                                                                                                                                                                                
                                                                     19                                                                                                                                                                                      

   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 2F50)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2F50)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F50)

(-) Gene Ontology  (14, 14)

Theoretical Model(hide GO term definitions)
Chain A   (GLO2_HUMAN | Q16775)
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:0004416    hydroxyacylglutathione hydrolase activity    Catalysis of the reaction: (S)-(2-hydroxyacyl)glutathione + H2O = glutathione + a 2-hydroxy carboxylate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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).
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0006750    glutathione biosynthetic process    The chemical reactions and pathways resulting in the formation of glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins.
    GO:0006749    glutathione metabolic process    The chemical reactions and pathways involving glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide (H2O2) and oxidized ascorbate, and it participates in the gamma-glutamyl cycle.
    GO:0019243    methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione    The chemical reactions and pathways resulting in the breakdown of methylglyoxal, CH3-CO-CHO, into D-lactate via the intermediate S-lactoyl-glutathione. Glutathione is used in the first step of the pathway and then regenerated in the second step.
    GO:0006090    pyruvate metabolic process    The chemical reactions and pathways involving pyruvate, 2-oxopropanoate.
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: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:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

 Visualization

(-) Interactive Views

Theoretical Model
  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
    CE3  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 2f50)
 
  Cis Peptide Bonds
    Gly A:29 - Thr A:30   [ 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
  2f50
    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
  GLO2_HUMAN | Q16775
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.5.2.6
    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
  GLO2_HUMAN | Q16775
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        GLO2_HUMAN | Q167751qh3 1qh5

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2F50)