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(-) Description

Title :  CRYSTAL STRUCTURE OF N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE (GLMU) FROM MYCOBACTERIUM TUBERCULOSIS IN A CUBIC SPACE GROUP.
 
Authors :  S. K. Verma, B. Prakash
Date :  31 Dec 08  (Deposition) - 09 Jun 09  (Release) - 09 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.41
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Acetyltransferase, Bifunctional, Pyrophosphorylase, Rossmann- Like Fold, Left-Handed-Beta-Helix, Trimer, Acyltransferase, Cell Shape, Cell Wall Biogenesis/Degradation, Cytoplasm, Magnesium, Metal-Binding, Multifunctional Enzyme, Nucleotidyltransferase, Peptidoglycan Synthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. K. Verma, M. Jaiswal, N. Kumar, A. Parikh, V. K. Nandicoori, B. Prakash
Structure Of N-Acetylglucosamine-1-Phosphate Uridyltransferase (Glmu) From Mycobacterium Tuberculosis In A Cubic Space Group.
Acta Crystallogr. , Sect. F V. 65 435 2009
PubMed-ID: 19407371  |  Reference-DOI: 10.1107/S1744309109010252
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BIFUNCTIONAL PROTEIN GLMU
    ChainsA
    EC Number2.7.7.23, 2.3.1.157
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQEII
    Expression System StrainDH5ALPHA
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneGLMU, MRA_1026, MT1046, RV1018C
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid1773
    StrainH37RV
    SynonymUDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE, N- ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE, GLUCOSAMINE-1-PHOSPHATE N-ACETYLTRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (3x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1SO412Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:344 , PRO A:345BINDING SITE FOR RESIDUE SO4 A 496
2AC2SOFTWAREASP A:307 , ARG A:323 , THR A:324 , PHE A:340BINDING SITE FOR RESIDUE SO4 A 497
3AC3SOFTWAREGLY A:435 , VAL A:437 , SER A:450 , ALA A:451 , GLY A:452BINDING SITE FOR RESIDUE SO4 A 498
4AC4SOFTWAREARG A:34 , HIS A:42 , LYS A:46BINDING SITE FOR RESIDUE SO4 A 499

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:338 -Pro A:339
2Ala A:422 -Pro A:423
3Ala A:471 -Gln A:472

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FOQ)

(-) Exons   (0, 0)

(no "Exon" information available for 3FOQ)

(-) 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:439
 aligned with GLMU_MYCTO | P9WMN2 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:473
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470   
           GLMU_MYCTO     1 MTFPGDTAVLVLAAGPGTRMRSDTPKVLHTLAGRSMLSHVLHAIAKLAPQRLIVVLGHDHQRIAPLVGELADTLGRTIDVALQDRPLGTGHAVLCGLSALPDDYAGNVVVTSGDTPLLDADTLADLIATHRAVSAAVTVLTTTLDDPFGYGRILRTQDHEVMAIVEQTDATPSQREIREVNAGVYAFDIAALRSALSRLSSNNAQQELYLTDVIAILRSDGQTVHASHVDDSALVAGVNNRVQLAELASELNRRVVAAHQLAGVTVVDPATTWIDVDVTIGRDTVIHPGTQLLGRTQIGGRCVVGPDTTLTDVAVGDGASVVRTHGSSSSIGDGAAVGPFTYLRPGTALGADGKLGAFVEVKNSTIGTGTKVPHLTYVGDADIGEYSNIGASSVFVNYDGTSKRRTTVGSHVRTGSDTMFVAPVTIGDGAYTGAGTVVREDVPPGALAVSAGPQRNIENWVQRKRPGSPAAQA 473
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee...........hhhh.ee..eehhhhhhhhhhhhh..eeeeee............hhhhhhh...eeee.....hhhhhhhhhhh........eeeeee......hhhhhhhhhhhhhhh...eeeeee...------.eee.....eeee.-.-----------.eeeeeeeeehhhhhhhhh.---------..hhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhhhhhhhhhhhheee......ee.........eee....eee...ee....ee....eee..ee....ee..eeee.eee....ee...eeee..eee....ee...eeee..ee....ee...eeee.eee..........eee.-------.eee..........eee.........ee....ee........ee...........hhhhhh.hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3foq A   1 MTFPGDTAVLVLAAGPGTRMRSDTPKVLHTLAGRSMLSHVLHAIAKLAPQRLIVVLGHDHQRIAPLVGELADTLGRTIDVALQDRPLGTGHAVLCGLSALPDDYAGNVVVTSGDTPLLDADTLADLIATHRAVSAAVTVLTTTLD------RILRTQDHEVMAIV-Q-----------EVNAGVYAFDIAALRSALSR---------LYLTDVIAILRSDGQTVHASHVDDSALVAGVNNRVQLAELASELNRRVVAAHQLAGVTVVDPATTWIDVDVTIGRDTVIHPGTQLLGRTQIGGRCVVGPDTTLTDVAVGDGASVVRTHGSSSSIGDGAAVGPFTYLRPGTALGADGKLGAFVEVKNSTIGTGTKVPHLTYVGDADIGEYSNIGASSVFVN-------RTTVGSHVRTGSDTMFVAPVTIGDGAYTGAGTVVREDVPPGALAVSAGPQRNIENWVQRKRPGSPAAQA 473
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    |    - |     160    | |  -       180       190       | -       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390      |  -    |  410       420       430       440       450       460       470   
                                                                                                                                                                          145    152          165 |         179                198       208                                                                                                                                                                                          397     405                                                                    
                                                                                                                                                                                                167                                                                                                                                                                                                                                                                                                                  

Chain A from PDB  Type:PROTEIN  Length:439
 aligned with GLMU_MYCTU | P9WMN3 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:473
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470   
           GLMU_MYCTU     1 MTFPGDTAVLVLAAGPGTRMRSDTPKVLHTLAGRSMLSHVLHAIAKLAPQRLIVVLGHDHQRIAPLVGELADTLGRTIDVALQDRPLGTGHAVLCGLSALPDDYAGNVVVTSGDTPLLDADTLADLIATHRAVSAAVTVLTTTLDDPFGYGRILRTQDHEVMAIVEQTDATPSQREIREVNAGVYAFDIAALRSALSRLSSNNAQQELYLTDVIAILRSDGQTVHASHVDDSALVAGVNNRVQLAELASELNRRVVAAHQLAGVTVVDPATTWIDVDVTIGRDTVIHPGTQLLGRTQIGGRCVVGPDTTLTDVAVGDGASVVRTHGSSSSIGDGAAVGPFTYLRPGTALGADGKLGAFVEVKNSTIGTGTKVPHLTYVGDADIGEYSNIGASSVFVNYDGTSKRRTTVGSHVRTGSDTMFVAPVTIGDGAYTGAGTVVREDVPPGALAVSAGPQRNIENWVQRKRPGSPAAQA 473
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee...........hhhh.ee..eehhhhhhhhhhhhh..eeeeee............hhhhhhh...eeee.....hhhhhhhhhhh........eeeeee......hhhhhhhhhhhhhhh...eeeeee...------.eee.....eeee.-.-----------.eeeeeeeeehhhhhhhhh.---------..hhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhhhhhhhhhhhheee......ee.........eee....eee...ee....ee....eee..ee....ee..eeee.eee....ee...eeee..eee....ee...eeee..ee....ee...eeee.eee..........eee.-------.eee..........eee.........ee....ee........ee...........hhhhhh.hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3foq A   1 MTFPGDTAVLVLAAGPGTRMRSDTPKVLHTLAGRSMLSHVLHAIAKLAPQRLIVVLGHDHQRIAPLVGELADTLGRTIDVALQDRPLGTGHAVLCGLSALPDDYAGNVVVTSGDTPLLDADTLADLIATHRAVSAAVTVLTTTLD------RILRTQDHEVMAIV-Q-----------EVNAGVYAFDIAALRSALSR---------LYLTDVIAILRSDGQTVHASHVDDSALVAGVNNRVQLAELASELNRRVVAAHQLAGVTVVDPATTWIDVDVTIGRDTVIHPGTQLLGRTQIGGRCVVGPDTTLTDVAVGDGASVVRTHGSSSSIGDGAAVGPFTYLRPGTALGADGKLGAFVEVKNSTIGTGTKVPHLTYVGDADIGEYSNIGASSVFVN-------RTTVGSHVRTGSDTMFVAPVTIGDGAYTGAGTVVREDVPPGALAVSAGPQRNIENWVQRKRPGSPAAQA 473
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    |    - |     160    | |  -       180       190       | -       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390      |  -    |  410       420       430       440       450       460       470   
                                                                                                                                                                          145    152          165 |         179                198       208                                                                                                                                                                                          397     405                                                                    
                                                                                                                                                                                                167                                                                                                                                                                                                                                                                                                                  

   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 3FOQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FOQ)

(-) Gene Ontology  (19, 36)

Asymmetric Unit(hide GO term definitions)
Chain A   (GLMU_MYCTU | P9WMN3)
molecular function
    GO:0003977    UDP-N-acetylglucosamine diphosphorylase activity    Catalysis of the reaction: N-acetyl-alpha-D-glucosamine 1-phosphate + UTP = diphosphate + UDP-N-acetyl-alpha-D-glucosamine.
    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:0019134    glucosamine-1-phosphate N-acetyltransferase activity    Catalysis of the reaction: alpha-D-glucosamine 1-phosphate + acetyl-CoA = N-acetyl-alpha-D-glucosamine 1-phosphate + CoA + H(+).
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
    GO:0070569    uridylyltransferase activity    Catalysis of the transfer of an uridylyl group to an acceptor.
biological process
    GO:0006048    UDP-N-acetylglucosamine biosynthetic process    The chemical reactions and pathways resulting in the formation of UDP-N-acetylglucosamine, a substance composed of N-acetylglucosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate.
    GO:0000902    cell morphogenesis    The developmental process in which the size or shape of a cell is generated and organized.
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    GO:0009245    lipid A biosynthetic process    The chemical reactions and pathways resulting in the formation of lipid A, the glycolipid group of bacterial lipopolysaccharides, consisting of four to six fatty acyl chains linked to two glucosamine residues. Further modifications of the backbone are common.
    GO:0009103    lipopolysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
    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:0009252    peptidoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A   (GLMU_MYCTO | P9WMN2)
molecular function
    GO:0003977    UDP-N-acetylglucosamine diphosphorylase activity    Catalysis of the reaction: N-acetyl-alpha-D-glucosamine 1-phosphate + UTP = diphosphate + UDP-N-acetyl-alpha-D-glucosamine.
    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:0019134    glucosamine-1-phosphate N-acetyltransferase activity    Catalysis of the reaction: alpha-D-glucosamine 1-phosphate + acetyl-CoA = N-acetyl-alpha-D-glucosamine 1-phosphate + CoA + H(+).
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
    GO:0006048    UDP-N-acetylglucosamine biosynthetic process    The chemical reactions and pathways resulting in the formation of UDP-N-acetylglucosamine, a substance composed of N-acetylglucosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate.
    GO:0000902    cell morphogenesis    The developmental process in which the size or shape of a cell is generated and organized.
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0009245    lipid A biosynthetic process    The chemical reactions and pathways resulting in the formation of lipid A, the glycolipid group of bacterial lipopolysaccharides, consisting of four to six fatty acyl chains linked to two glucosamine residues. Further modifications of the backbone are common.
    GO:0009103    lipopolysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
    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:0009252    peptidoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GLMU_MYCTO | P9WMN22qkx 3d8v 3d98 3dj4 3spt 3st8 4g3p 4g3q 4g3s 4g87 4hcq 4k6r
        GLMU_MYCTU | P9WMN32qkx 3d8v 3d98 3dj4 3spt 3st8 4g3p 4g3q 4g3s 4g87 4hcq 4k6r

(-) Related Entries Specified in the PDB File

3dk5 CRYSTAL STRUCTURE OF APO-GLMU FROM MYCOBACTERIUM TUBERCULOSIS