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(-) Description

Title :  STRUCTURE OF MTB 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLTRANSFERASE (ISPD) COMPLEXED WITH CDP-ME
 
Authors :  M. C. M. Reddy, J. B. Bruning, C. Thurman, T. R. Ioerger, J. C. Sacchettin Structural Genomics Consortium (Tbsgc)
Date :  05 Jan 11  (Deposition) - 04 May 11  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tb Structural Genomics Consortium, Tbsgc, Rossmann Fold, 2-C-Methyl- D-Erythritol 4-Phosphate Cytidyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. C. M. Reddy, J. B. Bruning, C. Thurman, T. R. Ioerger, J. C. Sacchettini
Crystal Structure Of Mycobacterium Tuberculosis 2-C-Methyl-D-Erythritol 4-Phosphate Cytidyltransferase (Ispd): A Candidate Antitubercular Drug Target
Proteins 2011
PubMed: search

(-) Compounds

Molecule 1 - 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLTRANSFERASE
    ChainsA, B
    EC Number2.7.7.60
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneISPD, RV3582C, MT3688, MTCY06G11.29C
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid83332
    StrainH37RV
    Synonym4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL SYNTHASE, MEP CYTIDYLYLTRANSFERASE, MCT

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1CDM2Ligand/Ion4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL
2CL4Ligand/IonCHLORIDE ION
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:13 , ALA A:14 , ALA A:15 , GLY A:16 , LYS A:27 , GLY A:80 , SER A:81 , ASN A:82 , ARG A:83 , THR A:86 , ASP A:107 , ALA A:108 , ALA A:109 , ARG A:110 , VAL A:163 , THR A:191 , ASP A:192 , LYS A:215 , MG A:232 , HOH A:265 , HOH A:269 , HOH A:328 , HOH A:385 , HOH A:386 , HOH A:388 , HOH A:391 , HOH A:399 , HOH A:404 , HOH A:414 , ASP B:140 , THR B:141 , ARG B:157BINDING SITE FOR RESIDUE CDM A 500
2AC2SOFTWAREHOH A:328 , HOH A:385 , HOH A:386 , HOH A:414 , CDM A:500BINDING SITE FOR RESIDUE MG A 232
3AC3SOFTWAREGLY A:16 , SER A:17 , GLY A:18 , HOH A:386 , HOH A:403 , HOH A:404BINDING SITE FOR RESIDUE CL A 233
4AC4SOFTWARESER A:17 , GLU A:19 , ARG A:20 , HOH A:328BINDING SITE FOR RESIDUE CL A 234
5AC5SOFTWAREASP A:140 , THR A:141 , ARG A:157 , HOH A:336 , HOH A:382 , PRO B:13 , ALA B:14 , ALA B:15 , GLY B:16 , LYS B:27 , GLY B:80 , SER B:81 , ASN B:82 , ARG B:83 , THR B:86 , ASP B:107 , ALA B:108 , ALA B:109 , ARG B:110 , VAL B:163 , THR B:165 , THR B:191 , LYS B:215 , MG B:232 , CL B:233 , HOH B:253 , HOH B:274 , HOH B:343 , HOH B:380 , HOH B:390 , HOH B:391 , HOH B:392 , HOH B:394BINDING SITE FOR RESIDUE CDM B 501
6AC6SOFTWAREHOH B:278 , HOH B:390 , HOH B:391 , HOH B:392 , HOH B:394 , CDM B:501BINDING SITE FOR RESIDUE MG B 232
7AC7SOFTWAREGLY B:16 , SER B:17 , GLY B:18 , LYS B:27 , HOH B:390 , CDM B:501BINDING SITE FOR RESIDUE CL B 233
8AC8SOFTWAREGLY B:18 , GLU B:19 , ARG B:20 , LEU B:21 , LYS B:27 , HOH B:381BINDING SITE FOR RESIDUE CL B 234

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q80)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Thr A:165 -Pro A:166
2Thr B:165 -Pro B:166
3Ala B:188 -Glu B:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q80)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ISPDPS01295 4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature.ISPD_MYCTO103-110
 
  2A:103-110
B:103-110
ISPD_MYCTU103-110
 
  2A:103-110
B:103-110

(-) Exons   (0, 0)

(no "Exon" information available for 3Q80)

(-) Sequences/Alignments

Asymmetric/Biological 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:218
 aligned with ISPD_MYCTO | P9WKG8 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:226
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225      
           ISPD_MYCTO     6 GEVVAIVPAAGSGERLAVGVPKAFYQLDGQTLIERAVDGLLDSGVVDTVVVAVPADRTDEARQILGHRAMIVAGGSNRTDTVNLALTVLSGTAEPEFVLVHDAARALTPPALVARVVEALRDGYAAVVPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTPQGFTTDLLLRSYQRGSLDLPAAEYTDDASLVEHIGGQVQVVDGDPLAFKITTKLDLLLAQAIVRG 231
               SCOP domains d3q80a_ A: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee............hhhh.ee..eehhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhheeee...hhhhhhhhhhhhhh---...eeee........hhhhhhhhhhhhhh...eeeeee.....eeee.....eee..hhh.eeee...eeeehhhhhhhhhhhh.-----....hhhhhhhh....eeee.hhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------------------ISPD    ------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q80 A   6 GEVVAIVPAAGSGERLAVGVPKAFYQLDGQTLIERAVDGLLDSGVVDTVVVAVPADRTDEARQILGHRAMIVAGGSNRTDTVNLALTVLS---EPEFVLVHDAARALTPPALVARVVEALRDGYAAVVPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTPQGFTTDLLLRSYQRGSL-----EYTDDASLVEHIGGQVQVVDGDPLAFKITTKLDLLLAQAIVRG 231
                                    15        25        35        45        55        65        75        85        95   |   105       115       125       135       145       155       165       175       | -   |   195       205       215       225      
                                                                                                                    95  99                                                                                 183   189                                          

Chain A from PDB  Type:PROTEIN  Length:218
 aligned with ISPD_MYCTU | P9WKG9 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:226
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225      
           ISPD_MYCTU     6 GEVVAIVPAAGSGERLAVGVPKAFYQLDGQTLIERAVDGLLDSGVVDTVVVAVPADRTDEARQILGHRAMIVAGGSNRTDTVNLALTVLSGTAEPEFVLVHDAARALTPPALVARVVEALRDGYAAVVPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTPQGFTTDLLLRSYQRGSLDLPAAEYTDDASLVEHIGGQVQVVDGDPLAFKITTKLDLLLAQAIVRG 231
               SCOP domains d3q80a_ A: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee............hhhh.ee..eehhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhheeee...hhhhhhhhhhhhhh---...eeee........hhhhhhhhhhhhhh...eeeeee.....eeee.....eee..hhh.eeee...eeeehhhhhhhhhhhh.-----....hhhhhhhh....eeee.hhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------ISPD    ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q80 A   6 GEVVAIVPAAGSGERLAVGVPKAFYQLDGQTLIERAVDGLLDSGVVDTVVVAVPADRTDEARQILGHRAMIVAGGSNRTDTVNLALTVLS---EPEFVLVHDAARALTPPALVARVVEALRDGYAAVVPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTPQGFTTDLLLRSYQRGSL-----EYTDDASLVEHIGGQVQVVDGDPLAFKITTKLDLLLAQAIVRG 231
                                    15        25        35        45        55        65        75        85        95   |   105       115       125       135       145       155       165       175       | -   |   195       205       215       225      
                                                                                                                    95  99                                                                                 183   189                                          

Chain B from PDB  Type:PROTEIN  Length:218
 aligned with ISPD_MYCTO | P9WKG8 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:226
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225      
           ISPD_MYCTO     6 GEVVAIVPAAGSGERLAVGVPKAFYQLDGQTLIERAVDGLLDSGVVDTVVVAVPADRTDEARQILGHRAMIVAGGSNRTDTVNLALTVLSGTAEPEFVLVHDAARALTPPALVARVVEALRDGYAAVVPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTPQGFTTDLLLRSYQRGSLDLPAAEYTDDASLVEHIGGQVQVVDGDPLAFKITTKLDLLLAQAIVRG 231
               SCOP domains d3q80b_ B: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --IspD-3q80B01 B:8-231                                                                                                                                                                                                             Pfam domains (1)
           Pfam domains (2) --IspD-3q80B02 B:8-231                                                                                                                                                                                                             Pfam domains (2)
         Sec.struct. author ..eeeeee............hhhh.ee..eehhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhheeee...hhhhhhhhhhhh.----...eeee........hhhhhhhhhhhhhh...eeeeee.....eeee.....eee..hhh.eeee...eeeehhhhhhhhhh----........hhhhhhhh....eeee.hhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------------------ISPD    ------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q80 B   6 GEVVAIVPAAGSGERLAVGVPKAFYQLDGQTLIERAVDGLLDSGVVDTVVVAVPADRTDEARQILGHRAMIVAGGSNRTDTVNLALTVL----EPEFVLVHDAARALTPPALVARVVEALRDGYAAVVPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTPQGFTTDLLLRSYQR----LPAAEYTDDASLVEHIGGQVQVVDGDPLAFKITTKLDLLLAQAIVRG 231
                                    15        25        35        45        55        65        75        85        |-   |   105       115       125       135       145       155       165       175    |  185       195       205       215       225      
                                                                                                                   94   99                                                                              180  185                                              

Chain B from PDB  Type:PROTEIN  Length:218
 aligned with ISPD_MYCTU | P9WKG9 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:226
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225      
           ISPD_MYCTU     6 GEVVAIVPAAGSGERLAVGVPKAFYQLDGQTLIERAVDGLLDSGVVDTVVVAVPADRTDEARQILGHRAMIVAGGSNRTDTVNLALTVLSGTAEPEFVLVHDAARALTPPALVARVVEALRDGYAAVVPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTPQGFTTDLLLRSYQRGSLDLPAAEYTDDASLVEHIGGQVQVVDGDPLAFKITTKLDLLLAQAIVRG 231
               SCOP domains d3q80b_ B: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --IspD-3q80B01 B:8-231                                                                                                                                                                                                             Pfam domains (1)
           Pfam domains (2) --IspD-3q80B02 B:8-231                                                                                                                                                                                                             Pfam domains (2)
         Sec.struct. author ..eeeeee............hhhh.ee..eehhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhheeee...hhhhhhhhhhhh.----...eeee........hhhhhhhhhhhhhh...eeeeee.....eeee.....eee..hhh.eeee...eeeehhhhhhhhhh----........hhhhhhhh....eeee.hhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------ISPD    ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q80 B   6 GEVVAIVPAAGSGERLAVGVPKAFYQLDGQTLIERAVDGLLDSGVVDTVVVAVPADRTDEARQILGHRAMIVAGGSNRTDTVNLALTVL----EPEFVLVHDAARALTPPALVARVVEALRDGYAAVVPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTPQGFTTDLLLRSYQR----LPAAEYTDDASLVEHIGGQVQVVDGDPLAFKITTKLDLLLAQAIVRG 231
                                    15        25        35        45        55        65        75        85        |-   |   105       115       125       135       145       155       165       175    |  185       195       205       215       225      
                                                                                                                   94   99                                                                              180  185                                              

   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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q80)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: GT-A (172)

(-) Gene Ontology  (15, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ISPD_MYCTU | P9WKG9)
molecular function
    GO:0050518    2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity    Catalysis of the reaction: 2-C-methyl-D-erythritol 4-phosphate + CTP = 4-CDP-2-C-methyl-D-erythritol + diphosphate.
    GO:0002135    CTP binding    Interacting selectively and non-covalently with CTP, cytidine 5'-triphosphate.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    GO:0019288    isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway    The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate.
    GO:0051484    isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway involved in terpenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway that contributes to terpenoid biosynthesis. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate.
    GO:0008299    isoprenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
    GO:0016114    terpenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of terpenoids, any member of a class of compounds characterized by an isoprenoid chemical structure.
cellular component
    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.

Chain A,B   (ISPD_MYCTO | P9WKG8)
molecular function
    GO:0050518    2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity    Catalysis of the reaction: 2-C-methyl-D-erythritol 4-phosphate + CTP = 4-CDP-2-C-methyl-D-erythritol + diphosphate.
    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: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.
biological process
    GO:0019288    isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway    The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate.
    GO:0008299    isoprenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
    GO:0016114    terpenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of terpenoids, any member of a class of compounds characterized by an isoprenoid chemical structure.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ISPD_MYCTO | P9WKG82xwn 3okr 3q7u
        ISPD_MYCTU | P9WKG92xwn 3okr 3q7u

(-) Related Entries Specified in the PDB File

3okr APO MTB ISPD
3q7u MTB ISPD COMPLEXED WITH CTP