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(-) Description

Title :  EXTRACELLULAR DOMAIN OF MYCOBACTERIUM TUBERCULOSIS PKND
 
Authors :  M. C. Good, A. E. Greenstein, T. A. Young, H. L. Ng, T. Alber, Tb Structural Genomics Consortium (Tbsgc)
Date :  16 Dec 03  (Deposition) - 27 Apr 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Propeller, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. C. Good, A. E. Greenstein, T. A. Young, H. L. Ng, T. Alber
Sensor Domain Of The Mycobacterium Tuberculosis Receptor Ser/Thr Protein Kinase, Pknd, Forms A Highly Symmetric Beta Propeller.
J. Mol. Biol. V. 339 459 2004
PubMed-ID: 15136047  |  Reference-DOI: 10.1016/J.JMB.2004.03.063
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE PKND
    ChainsA
    EC Number2.7.1.37
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET24B
    Expression System StrainBL21 CODON +
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 403-665
    GenePKND, RV0931C, MT0958, MTCY08C9.08
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid1773

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1CD4Ligand/IonCADMIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:42BINDING SITE FOR RESIDUE CD A 501
2AC2SOFTWAREASP A:151 , ASP A:169 , HOH A:540BINDING SITE FOR RESIDUE CD A 502
3AC3SOFTWAREASP A:105 , HOH A:528BINDING SITE FOR RESIDUE CD A 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RWL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 6)

Asymmetric/Biological Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NHLPS51125 NHL repeat profile.PKND_MYCTO414-456
498-539
461-497
540-581
624-664
582-623
  6A:12-52
A:96-137
A:59-95
A:138-179
A:222-262
A:180-221
PKND_MYCTU414-456
498-539
461-497
540-581
624-664
582-623
  6A:12-52
A:96-137
A:59-95
A:138-179
A:222-262
A:180-221

(-) Exons   (0, 0)

(no "Exon" information available for 1RWL)

(-) 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:254
 aligned with PKND_MYCTO | P9WI78 from UniProtKB/Swiss-Prot  Length:664

    Alignment length:258
                                                                                                                                                                                                                                                                                     664      
                                   422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662 |      
           PKND_MYCTO   413 GQTVLPFTGIDFRLSPSGVAVDSAGNVYVTSEGMYGRVVKLATGSTGTTVLPFNGLYQPQGLAVDGAGTVYVTDFNNRVVTLAAGSNNQTVLPFDGLNYPEGLAVDTQGAVYVADRGNNRVVKLAAGSKTQTVLPFTGLNDPDGVAVDNSGNVYVTDTDNNRVVKLEAESNNQVVLPFTDITAPWGIAVDEAGTVYVTEHNTNQVVKLLAGSTTSTVLPFTGLNTPLAVAVDSDRTVYVADRGNDRVVKLTS------   -
               SCOP domains d1rwla_ A: Serine/threonine-protein kinase     PknD                                                                                                                                                                                                                SCOP domains
               CATH domains 1rwlA00 A:11-268 TolB, C-terminal domain                                                                                                                                                                                                                           CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NHL-1rwlA01 A:233-260       -------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NHL-1rwlA02 A:233-260       -------- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NHL-1rwlA03 A:233-260       -------- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NHL-1rwlA04 A:233-260       -------- Pfam domains (4)
           Pfam domains (5) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NHL-1rwlA05 A:233-260       -------- Pfam domains (5)
           Pfam domains (6) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NHL-1rwlA06 A:233-260       -------- Pfam domains (6)
         Sec.struct. author ..ee...........eeeeee.....eeeee.....eeeee.----..ee..........eeee.....eeeee...eeeee.......ee........eeeeee.....eeeee.hhheeeee.......ee............ee.....eeeeehhhheeeee......eee........eeeeee.....eeeee....eeeee.......ee............ee.....eeeeehhhheeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) -NHL  PDB: A:12-52 UniProt: 414-456         ----NHL  PDB: A:59-95 UniProt: 461-497   NHL  PDB: A:96-137 UniProt: 498-539       NHL  PDB: A:138-179 UniProt: 540-581      NHL  PDB: A:180-221 UniProt: 582-623      NHL  PDB: A:222-262 UniProt: 624-664     ------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1rwl A  11 GQTVLPFTGIDFRLSPSGVAVDSAGNVYVTSEGMYGRVVKLA----GTTVLPFNGLYQPQGLAVDGAGTVYVTDFNNRVVTLAAGSNNQTVLPFDGLNYPEGLAVDTQGAVYVADRGNNRVVKLAAGSKTQTVLPFTGLNDPDGVAVDNSGNVYVTDTDNNRVVKLEAESNNQVVLPFTDITAPWGIAVDEAGTVYVTEHNTNQVVKLLAGSTTSTVLPFTGLNTPLAVAVDSDRTVYVADRGNDRVVKLTSLEHHHH 268
                                    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        
                                                                    52   57                                                                                                                                                                                                                   

Chain A from PDB  Type:PROTEIN  Length:254
 aligned with PKND_MYCTU | P9WI79 from UniProtKB/Swiss-Prot  Length:664

    Alignment length:258
                                                                                                                                                                                                                                                                                     664      
                                   422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662 |      
           PKND_MYCTU   413 GQTVLPFTGIDFRLSPSGVAVDSAGNVYVTSEGMYGRVVKLATGSTGTTVLPFNGLYQPQGLAVDGAGTVYVTDFNNRVVTLAAGSNNQTVLPFDGLNYPEGLAVDTQGAVYVADRGNNRVVKLAAGSKTQTVLPFTGLNDPDGVAVDNSGNVYVTDTDNNRVVKLEAESNNQVVLPFTDITAPWGIAVDEAGTVYVTEHNTNQVVKLLAGSTTSTVLPFTGLNTPLAVAVDSDRTVYVADRGNDRVVKLTS------   -
               SCOP domains d1rwla_ A: Serine/threonine-protein kinase     PknD                                                                                                                                                                                                                SCOP domains
               CATH domains 1rwlA00 A:11-268 TolB, C-terminal domain                                                                                                                                                                                                                           CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NHL-1rwlA01 A:233-260       -------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NHL-1rwlA02 A:233-260       -------- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NHL-1rwlA03 A:233-260       -------- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NHL-1rwlA04 A:233-260       -------- Pfam domains (4)
           Pfam domains (5) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NHL-1rwlA05 A:233-260       -------- Pfam domains (5)
           Pfam domains (6) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NHL-1rwlA06 A:233-260       -------- Pfam domains (6)
         Sec.struct. author ..ee...........eeeeee.....eeeee.....eeeee.----..ee..........eeee.....eeeee...eeeee.......ee........eeeeee.....eeeee.hhheeeee.......ee............ee.....eeeeehhhheeeee......eee........eeeeee.....eeeee....eeeee.......ee............ee.....eeeeehhhheeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -NHL  PDB: A:12-52 UniProt: 414-456         ----NHL  PDB: A:59-95 UniProt: 461-497   NHL  PDB: A:96-137 UniProt: 498-539       NHL  PDB: A:138-179 UniProt: 540-581      NHL  PDB: A:180-221 UniProt: 582-623      NHL  PDB: A:222-262 UniProt: 624-664     ------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1rwl A  11 GQTVLPFTGIDFRLSPSGVAVDSAGNVYVTSEGMYGRVVKLA----GTTVLPFNGLYQPQGLAVDGAGTVYVTDFNNRVVTLAAGSNNQTVLPFDGLNYPEGLAVDTQGAVYVADRGNNRVVKLAAGSKTQTVLPFTGLNDPDGVAVDNSGNVYVTDTDNNRVVKLEAESNNQVVLPFTDITAPWGIAVDEAGTVYVTEHNTNQVVKLLAGSTTSTVLPFTGLNTPLAVAVDSDRTVYVADRGNDRVVKLTSLEHHHH 268
                                    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        
                                                                    52   57                                                                                                                                                                                                                   

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Family: NHL (2)
1aNHL-1rwlA01A:233-260
1bNHL-1rwlA02A:233-260
1cNHL-1rwlA03A:233-260
1dNHL-1rwlA04A:233-260
1eNHL-1rwlA05A:233-260
1fNHL-1rwlA06A:233-260

(-) Gene Ontology  (23, 35)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PKND_MYCTU | P9WI79)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    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: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:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    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:0016036    cellular response to phosphate starvation    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 deprivation of phosphate.
    GO:0043086    negative regulation of catalytic activity    Any process that stops or reduces the activity of an enzyme.
    GO:0045717    negative regulation of fatty acid biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of fatty acids.
    GO:0032091    negative regulation of protein binding    Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    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:0043085    positive regulation of catalytic activity    Any process that activates or increases the activity of an enzyme.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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   (PKND_MYCTO | P9WI78)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    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:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    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:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

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 Related Entries

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

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        PKND_MYCTO | P9WI781rwi
        PKND_MYCTU | P9WI791rwi

(-) Related Entries Specified in the PDB File

1rwi EXTRACELLULAR DOMAIN OF MYCOBACTERIUM TUBERCULOSIS PKND RELATED ID: RV0931C RELATED DB: TARGETDB