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(-) Description

Title :  CRYSTAL STRUCTURE OF GLMU FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
 
Authors :  Z. Zhang, C. J. Squire, E. N. Baker
Date :  25 May 08  (Deposition) - 10 Mar 09  (Release) - 10 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Nucleotide-Diphospho-Sugar Transferases/Single-Stranded Left-Handed Beta-Helix, Acyltransferase, Cell Shape, Cell Wall Biogenesis/Degradation, Cytoplasm, Magnesium, Metal- Binding, Multifunctional Enzyme, Nucleotidyltransferase, Peptidoglycan Synthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Z. Zhang, E. M. Bulloch, R. D. Bunker, E. N. Baker, C. J. Squire
Structure And Function Of Glmu From Mycobacterium Tuberculosis.
Acta Crystallogr. , Sect. D V. 65 275 2009
PubMed-ID: 19237750  |  Reference-DOI: 10.1107/S0907444909001036
(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 PlasmidPDEST17
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneGLMU, RV1018C, MT1046
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid1773
    Synonym[INCLUDES: UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE (EC 2.7.7.23) (N-ACETYLGLUCOSAMINE-1- PHOSPHATE URIDYLTRANSFERASE)

 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, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1UD11Ligand/IonURIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1UD13Ligand/IonURIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:12 , ALA A:14 , GLY A:15 , GLN A:83 , PRO A:86 , LEU A:87 , GLY A:88 , THR A:89 , ALA A:92 , SER A:112 , TYR A:150 , GLY A:151 , GLU A:166 , ASN A:181 , THR A:211 , ASN A:239 , HOH A:497 , HOH A:517 , HOH A:586BINDING SITE FOR RESIDUE UD1 A 496

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D8V)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Met A:1 -Thr A:2
2Gly A:5 -Asp A:6
3Gly A:305 -Pro A:306
4Gly A:338 -Pro A:339
5Ala A:422 -Pro A:423

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D8V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3D8V)

(-) Exons   (0, 0)

(no "Exon" information available for 3D8V)

(-) 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:478
 aligned with GLMU_MYCTO | P9WMN2 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:479
                                    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 MTFPGDTAVLVLAAGPGTRMRSDTPKVLHTLAGRSMLSHVLHAIAKLAPQRLIVVLGHDHQRIAPLVGELADTLGRTIDVALQDRPLGTGHAVLCGLSALPDDYAGNVVVTSGDTPLLDADTLADLIATHRAVSAAVTVLTTTLDDPFGYGRILRTQDHEVMAIVEQTDATPSQREIREVNAGVYAFDIAALRSALSRLSSNNAQQELYLTDVIAILRSDGQTVHASHVDDSALVAGVNNRVQLAELASELNRRVVAAHQLAGVTVVDPATTWIDVDVTIGRDTVIHPGTQLLGRTQIGGRCVVGPDTTLTDVAVGDGASVVRTHGSSSSIGDGAAVGPFTYLRPGTALGADGKLGAFVEVKNSTIGTGTKVPHLTYVGDADIGEYSNIGASSVFVNYDGTSKRRTTVGSHVRTGSDTMFVAPVTIGDGAYTGAGTVVREDVPPGALAVSAGPQRNIENWVQRKRPGSPAAQASKRASE 479
               SCOP domains d3d8va1 A:1-263 automated matches                                                                                                                                                                                                                                      d3d8va2 A:264-479 automated matches                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee....hhhhh...hhhh.ee..eehhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhh........eeeeee......hhhhhhhhhhhhhhh...eeeeeee........eeee.....eeeeehhhhh..hhhhh.eeeeeeeeeehhhhhhhhhh............hhhhhhhhhh...eeeee..hhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..ee.hhh.eee....ee....ee...eeee...ee....ee....eeeeeee....ee..eeeeeeee....ee...eee...eee....eeeeeeeee..ee....eeeeeeeee.eee....ee....eee...-.....eee....ee....eee...ee....ee....ee........ee..........hhhhhhh.....hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d8v A   1 MTFPGDTAVLVLAAGPGTRMRSDTPKVLHTLAGRSMLSHVLHAIAKLAPQRLIVVLGHDHQRIAPLVGELADTLGRTIDVALQDRPLGTGHAVLCGLSALPDDYAGNVVVTSGDTPLLDADTLADLIATHRAVSAAVTVLTTTLDDPFGYGRILRTQDHEVMAIVEQTDATPSQREIREVNAGVYAFDIAALRSALSRLSSNNAQQELYLTDVIAILRSDGQTVHASHVDDSALVAGVNNRVQLAELASELNRRVVAAHQLAGVTVVDPATTWIDVDVTIGRDTVIHPGTQLLGRTQIGGRCVVGPDTTLTDVAVGDGASVVRTHGSSSSIGDGAAVGPFTYLRPGTALGADGKLGAFVEVKNSTIGTGTKVPHLTYVGDADIGEYSNIGASSVFVNYD-TSKRRTTVGSHVRTGSDTMFVAPVTIGDGAYTGAGTVVREDVPPGALAVSAGPQRNIENWVQRKRPGSPAAQASKRASE 479
                                    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        |-|      410       420       430       440       450       460       470         
                                                                                                                                                                                                                                                                                                                                                                                                                                        399 |                                                                              
                                                                                                                                                                                                                                                                                                                                                                                                                                          401                                                                              

Chain A from PDB  Type:PROTEIN  Length:478
 aligned with GLMU_MYCTU | P9WMN3 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:479
                                    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 MTFPGDTAVLVLAAGPGTRMRSDTPKVLHTLAGRSMLSHVLHAIAKLAPQRLIVVLGHDHQRIAPLVGELADTLGRTIDVALQDRPLGTGHAVLCGLSALPDDYAGNVVVTSGDTPLLDADTLADLIATHRAVSAAVTVLTTTLDDPFGYGRILRTQDHEVMAIVEQTDATPSQREIREVNAGVYAFDIAALRSALSRLSSNNAQQELYLTDVIAILRSDGQTVHASHVDDSALVAGVNNRVQLAELASELNRRVVAAHQLAGVTVVDPATTWIDVDVTIGRDTVIHPGTQLLGRTQIGGRCVVGPDTTLTDVAVGDGASVVRTHGSSSSIGDGAAVGPFTYLRPGTALGADGKLGAFVEVKNSTIGTGTKVPHLTYVGDADIGEYSNIGASSVFVNYDGTSKRRTTVGSHVRTGSDTMFVAPVTIGDGAYTGAGTVVREDVPPGALAVSAGPQRNIENWVQRKRPGSPAAQASKRASE 479
               SCOP domains d3d8va1 A:1-263 automated matches                                                                                                                                                                                                                                      d3d8va2 A:264-479 automated matches                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee....hhhhh...hhhh.ee..eehhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhh........eeeeee......hhhhhhhhhhhhhhh...eeeeeee........eeee.....eeeeehhhhh..hhhhh.eeeeeeeeeehhhhhhhhhh............hhhhhhhhhh...eeeee..hhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..ee.hhh.eee....ee....ee...eeee...ee....ee....eeeeeee....ee..eeeeeeee....ee...eee...eee....eeeeeeeee..ee....eeeeeeeee.eee....ee....eee...-.....eee....ee....eee...ee....ee....ee........ee..........hhhhhhh.....hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d8v A   1 MTFPGDTAVLVLAAGPGTRMRSDTPKVLHTLAGRSMLSHVLHAIAKLAPQRLIVVLGHDHQRIAPLVGELADTLGRTIDVALQDRPLGTGHAVLCGLSALPDDYAGNVVVTSGDTPLLDADTLADLIATHRAVSAAVTVLTTTLDDPFGYGRILRTQDHEVMAIVEQTDATPSQREIREVNAGVYAFDIAALRSALSRLSSNNAQQELYLTDVIAILRSDGQTVHASHVDDSALVAGVNNRVQLAELASELNRRVVAAHQLAGVTVVDPATTWIDVDVTIGRDTVIHPGTQLLGRTQIGGRCVVGPDTTLTDVAVGDGASVVRTHGSSSSIGDGAAVGPFTYLRPGTALGADGKLGAFVEVKNSTIGTGTKVPHLTYVGDADIGEYSNIGASSVFVNYD-TSKRRTTVGSHVRTGSDTMFVAPVTIGDGAYTGAGTVVREDVPPGALAVSAGPQRNIENWVQRKRPGSPAAQASKRASE 479
                                    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        |-|      410       420       430       440       450       460       470         
                                                                                                                                                                                                                                                                                                                                                                                                                                        399 |                                                                              
                                                                                                                                                                                                                                                                                                                                                                                                                                          401                                                                              

   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 Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3D8V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D8V)

(-) Gene Ontology  (19, 36)

Asymmetric Unit(hide GO term definitions)
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.

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.

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

2qkx CRYSTAL STRUCTURE OF GLMU FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH N-ACETYL GLUCOSAMINE 1-PHOSPHATE
3d98 CRYSTAL STRUCTURE OF GLMU FROM MYCOBACTERIUM TUBERCULOSIS, LIGAND-FREE FORM