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(-) Description

Title :  CATION PROMOTED ASSOCIATION (CPA) OF A REGULATORY AND TARGET PROTEIN IS CONTROLLED BY PHOSPHORYLATION
 
Authors :  M. D. Feese, N. D. Meadow, S. Roseman, D. W. Pettigrew, S. J. Remington
Date :  07 Mar 94  (Deposition) - 31 May 94  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.93
Chains :  Asym. Unit :  F,G
Biol. Unit 1:  F,G  (4x)
Keywords :  Phosphotransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Feese, D. W. Pettigrew, N. D. Meadow, S. Roseman, S. J. Remington
Cation-Promoted Association Of A Regulatory And Target Protein Is Controlled By Protein Phosphorylation.
Proc. Natl. Acad. Sci. Usa V. 91 3544 1994
PubMed-ID: 8170944  |  Reference-DOI: 10.1073/PNAS.91.9.3544
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUCOSE-SPECIFIC PROTEIN IIIGLC
    ChainsF
    EC Number2.7.1.69
    EngineeredYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
 
Molecule 2 - GLYCEROL KINASE
    ChainsG
    EC Number2.7.1.30
    EngineeredYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit FG
Biological Unit 1 (4x)FG

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2G3H1Ligand/IonGLYCERALDEHYDE-3-PHOSPHATE
3MN1Ligand/IonMANGANESE (II) ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1ADP4Ligand/IonADENOSINE-5'-DIPHOSPHATE
2G3H4Ligand/IonGLYCERALDEHYDE-3-PHOSPHATE
3MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP G:10 , ARG G:17 , ASP G:245 , G3H G:503 , ADP G:504 , HOH G:510BINDING SITE FOR RESIDUE MN G 502
2AC2SOFTWARETHR G:13 , ARG G:83 , GLU G:84 , TYR G:135 , ASP G:245 , GLN G:246 , THR G:267 , PHE G:270 , MN G:502 , ADP G:504 , HOH G:510BINDING SITE FOR RESIDUE G3H G 503
3AC3SOFTWARETHR G:14 , ARG G:17 , GLY G:266 , THR G:267 , GLY G:310 , ALA G:311 , ALA G:326 , TYR G:327 , GLY G:411 , ALA G:412 , ASN G:415 , MN G:502 , G3H G:503 , HOH G:510BINDING SITE FOR RESIDUE ADP G 504
4MN1AUTHORASP G:10 , G3H G:503 , ADP G:504 , MN G:502MN(II) BINDING SITE AT THE ACTIVE SITE OF GLYCEROL KINASE

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala G:353 -Pro G:354

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GLD)

(-) PROSITE Motifs  (4, 4)

Asymmetric Unit (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PTS_EIIA_TYPE_1PS51093 PTS_EIIA type-1 domain profile.PTGA_ECOLI39-143  1F:38-142
2PTS_EIIA_TYPE_1_HISPS00371 PTS EIIA domains phosphorylation site signature 1.PTGA_ECOLI85-97  1F:84-96
3FGGY_KINASES_1PS00933 FGGY family of carbohydrate kinases signature 1.GLPK_ECOLI136-148  1G:135-147
4FGGY_KINASES_2PS00445 FGGY family of carbohydrate kinases signature 2.GLPK_ECOLI363-383  1G:362-382
Biological Unit 1 (4, 16)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PTS_EIIA_TYPE_1PS51093 PTS_EIIA type-1 domain profile.PTGA_ECOLI39-143  4F:38-142
2PTS_EIIA_TYPE_1_HISPS00371 PTS EIIA domains phosphorylation site signature 1.PTGA_ECOLI85-97  4F:84-96
3FGGY_KINASES_1PS00933 FGGY family of carbohydrate kinases signature 1.GLPK_ECOLI136-148  4G:135-147
4FGGY_KINASES_2PS00445 FGGY family of carbohydrate kinases signature 2.GLPK_ECOLI363-383  4G:362-382

(-) Exons   (0, 0)

(no "Exon" information available for 1GLD)

(-) 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 F from PDB  Type:PROTEIN  Length:161
 aligned with PTGA_ECOLI | P69783 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161        
           PTGA_ECOLI     2 GLFDKLKSLVSDDKKDTGTIEIIAPLSGEIVNIEDVPDVVFAEKIVGDGIAIKPTGNKMVAPVDGTIGKIFETNHAFSIESDSGVELFVHFGIDTVELKGEGFKRIAEEGQRVKVGDTVIEFDLPLLEEKAKSTLTPVVISNMDEIKELIKLSGSVTVGETPVIRIKK 169
               SCOP domains d1gldf_ F:        Glucose-specific factor III (glsIII)                                                                                                                   SCOP domains
               CATH domains 1gldF00 F:1       -168 Glucose Permease (Domain IIA)                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
     Sec.struct. author (1) ...........-------.eee.....eee.hhhhh.hhhhhh....eeeeee...eeeee..eeeeeeee...eeeeeeee.eeeeeeee..hhhhhh..eeeee....eee.....----hhhhhhhh.....------hhhhheeeeee.eee......eeeee. Sec.struct. author (1)
     Sec.struct. author (2) ----------------------------------------------------------------------------------------------------------------------eeeee------------eeeeeee-------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -------------------------------------PTS_EIIA_TYPE_1  PDB: F:38-142 UniProt: 39-143                                                           -------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------PTS_EIIA_TYPE------------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1gld F   1 GLFDKLKSLVS-------TIEIIAPLSGEIVNIEDVPDVVFAEKIVGDGIAIKPTGNKMVAPVDGTIGKIFETNHAFSIESDSGVELFVHFGIDTVELKGEGFKRIAEEGQRVKVGDTVIEFDLPLLEEKAKSTLTPVVISNMDEIKELIKLSGSVTVGETPVIRIKK 168
                                    10|       20        30        40        50        60        70        80        90       100       110       120       130       140       150       160        
                                     11      19                                                                                                                                                     

Chain G from PDB  Type:PROTEIN  Length:489
 aligned with GLPK_ECOLI | P0A6F3 from UniProtKB/Swiss-Prot  Length:502

    Alignment length:496
                                    14        24        34        44        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       364       374       384       394       404       414       424       434       444       454       464       474       484       494      
           GLPK_ECOLI     5 KYIVALDQGTTSSRAVVMDHDANIISVSQREFEQIYPKPGWVEHDPMEIWATQSSTLVEVLAKADISSDQIAAIGITNQRETTIVWEKETGKPIYNAIVWQCRRTAEICEHLKRDGLEDYIRSNTGLVIDPYFSGTKVKWILDHVEGSRERARRGELLFGTVDTWLIWKMTQGRVHVTDYTNASRTMLFNIHTLDWDDKMLEVLDIPREMLPEVRRSSEVYGQTNIGGKGGTRIPISGIAGDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAVKSENGLLTTIACGPTGEVNYALEGAVFMAGASIQWLRDEMKLINDAYDSEYFATKVQNTNGVYVVPAFTGLGAPYWDPYARGAIFGLTRGVNANHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLMQFQSDILGTRVERPEVREVTALGAAYLAGLAVGFWQNLDELQEKAVIEREFRPGIETTERNYRYAGWKKAVKRAMAWEEH 500
               SCOP domains d1gldg1 G:4-253 Glycerol kinase                                                                                                                                                                                                                           d1gldg2 G:254-499 Glycerol kinase                                                                                                                                                                                                                      SCOP domains
               CATH domains 1gldG01 G:4-253  [code=3.30.420.40, no name defined]                                                                                                                                                                                                      1gldG02 G:254-499  [code=3.30.420.40, no name defined]                                                                                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeeeeeee...eeeeeee.......eeeee..eeee....eeeeehhhhhhhhhhhhhhhhhh.........eeeeee....eeeee...eeeeeeee......hhhhhhhhhh...hhhhhh...........hhhhhhhhhh....hhhhhhh..eee.hhhhhhhhhhh...eee.hhhhhh...ee....ee..hhhhh.........eee......eee..-------eeeeeee.hhhhhhhhh......eeeeee...eeeeee...eeee....eeeeee.....eeeeeeeeee...hhhhhhhhhhh.....hhhhhhhhhh......eeee................eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhh......hhhhhh....eeee..hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_2       --------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gld G   4 KYIVALDQGTTSSRAVVMDHDANIISVSQREFEQIYPKPGWVEHDPMEIWATQSSTLVEVLAKADISSDQIAAIGITNQRETTIVWEKETGKPIYNAIVWQCRRTAEICEHLKRDGLEDYIRSNTGLVIDPYFSGTKVKWILDHVEGSRERARRGELLFGTVDTWLIWKMTQGRVHVTDYTNASRTMLFNIHTLDWDDKMLEVLDIPREMLPEVRRSSEVYGQTNI-------IPISGIAGDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAVKSENGLLTTIACGPTGEVNYALEGAVFMAGASIQWLRDEMKLINDAYDSEYFATKVQNTNGVYVVPAFTGLGAPYWDPYARGAIFGLTRGVNANHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLMQFQSDILGTRVERPEVREVTALGAAYLAGLAVGFWQNLDELQEKAVIEREFRPGIETTERNYRYAGWKKAVKRAMAWEEH 499
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223     |   -   |   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      
                                                                                                                                                                                                                                                           229     237                                                                                                                                                                                                                                                                      

   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, 3)

Asymmetric Unit

(-) CATH Domains  (2, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GLD)

(-) Gene Ontology  (27, 33)

Asymmetric Unit(hide GO term definitions)
Chain F   (PTGA_ECOLI | P69783)
molecular function
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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).
    GO:0090563    protein-phosphocysteine-sugar phosphotransferase activity    Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein S-phosphocysteine + sugar(out) = protein cysteine + sugar phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0034219    carbohydrate transmembrane transport    The process in which a carbohydrate is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0008643    carbohydrate transport    The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are any of a group of organic compounds based of the general formula Cx(H2O)y.
    GO:0045912    negative regulation of carbohydrate metabolic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate.
    GO:0009401    phosphoenolpyruvate-dependent sugar phosphotransferase system    The uptake and phosphorylation of specific carbohydrates from the extracellular environment; uptake and phosphorylation are coupled, making the PTS a link between the uptake and metabolism of sugars; phosphoenolpyruvate is the original phosphate donor; phosphoenolpyruvate passes the phosphate via a signal transduction pathway, to enzyme 1 (E1), which in turn passes it on to the histidine protein, HPr; the next step in the system involves sugar-specific membrane-bound complex, enzyme 2 (EII), which transports the sugar into the cell; it includes the sugar permease, which catalyzes the transport reactions; EII is usually divided into three different domains, EIIA, EIIB, and EIIC.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
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:0031234    extrinsic component of cytoplasmic side of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, 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.

Chain G   (GLPK_ECOLI | P0A6F3)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0004370    glycerol kinase activity    Catalysis of the reaction: ATP + glycerol = sn-glycerol 3-phosphate + ADP + 2 H(+).
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016773    phosphotransferase activity, alcohol group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
    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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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:0006974    cellular response to DNA damage 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 stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0019563    glycerol catabolic process    The chemical reactions and pathways resulting in the breakdown of glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
    GO:0006071    glycerol metabolic process    The chemical reactions and pathways involving glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
    GO:0006072    glycerol-3-phosphate metabolic process    The chemical reactions and pathways involving glycerol-3-phosphate, a phosphoric monoester of glycerol.
    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:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GLPK_ECOLI | P0A6F31bo5 1bot 1bu6 1bwf 1gla 1glb 1glc 1gle 1glf 1glj 1gll 3ezw
        PTGA_ECOLI | P697831f3g 1f3z 1ggr 1gla 1glb 1glc 1gle 1o2f 1o53 2f3g 2mp0 4jbw

(-) Related Entries Specified in the PDB File

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