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(-) Description

Title :  CRYSTAL STRUCTURE OF M. TUBERCULOSIS PKNB LEU33ASP/VAL222ASP DOUBLE MUTANT IN COMPLEX WITH ADP
 
Authors :  C. A Mieczkowski, T. Alber, Tb Structural Genomics Consortium (Tbsgc)
Date :  05 Nov 08  (Deposition) - 02 Dec 08  (Release) - 13 Jan 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Kinase, Pknb, Mycobacterium Tuberculosis, Structural Genomics, Pknb Kd Double Mutant Bound To Adp, Tb Structural Genomics Consortium, Tbsgc, Atp-Binding, Kinase, Magnesium, Metal-Binding, Nucleotide-Binding, Phosphoprotein, Serine/Threonine-Protein Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Mieczkowski, A. T. Iavarone, T. Alber
Auto-Activation Mechanism Of The Mycobacterium Tuberculosis Pknb Receptor Ser/Thr Kinase.
Embo J. V. 27 3186 2008
PubMed-ID: 19008858  |  Reference-DOI: 10.1038/EMBOJ.2008.236
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE PKNB
    ChainsA
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28B
    Expression System StrainBL21-CODON PLUS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentPKNB KINASE DOMAIN
    GeneMT0017, MTCY10H4.14C, PKNB, RV0014C
    MutationYES
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid1773
    StrainH37RV

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG4Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:18 , PHE A:19 , SER A:23 , VAL A:25 , LYS A:40 , MET A:92 , GLU A:93 , VAL A:95 , THR A:99 , LYS A:140 , ALA A:142 , ASN A:143 , MET A:145 , MET A:155 , ASP A:156 , MG A:310 , MG A:312 , HOH A:315 , HOH A:358 , HOH A:386 , HOH A:394 , HOH A:404 , HOH A:409 , HOH A:410 , HOH A:411 , HOH A:453BINDING SITE FOR RESIDUE ADP A 340
2AC2SOFTWAREASN A:143 , ASP A:156 , ADP A:340 , HOH A:410 , HOH A:411BINDING SITE FOR RESIDUE MG A 310
3AC3SOFTWAREPRO A:141 , ALA A:142 , HOH A:385 , HOH A:404BINDING SITE FOR RESIDUE MG A 311
4AC4SOFTWAREGLY A:20 , GLY A:21 , MET A:22 , SER A:23 , ADP A:340 , HOH A:394BINDING SITE FOR RESIDUE MG A 312
5AC5SOFTWAREASN A:127 , ALA A:267BINDING SITE FOR RESIDUE MG A 313

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F61)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3F61)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3F61)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.PKNB_MYCTO17-40  1A:17-40
PKNB_MYCTU17-40  1A:17-40
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.PKNB_MYCTO134-146  1A:134-146
PKNB_MYCTU134-146  1A:134-146

(-) Exons   (0, 0)

(no "Exon" information available for 3F61)

(-) 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:271
 aligned with PKNB_MYCTO | P9WI80 from UniProtKB/Swiss-Prot  Length:626

    Alignment length:290
                                    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
           PKNB_MYCTO     1 MTTPSHLSDRYELGEILGFGGMSEVHLARDLRLHRDVAVKVLRADLARDPSFYLRFRREAQNAAALNHPAIVAVYDTGEAETPAGPLPYIVMEYVDGVTLRDIVHTEGPMTPKRAIEVIADACQALNFSHQNGIIHRDVKPANIMISATNAVKVMDFGIARAIADSGNSVTQTAAVIGTAQYLSPEQARGDSVDARSDVYSLGCVLYEVLTGEPPFTGDSPVSVAYQHVREDPIPPSARHEGLSADLDAVVLKALAKNPENRYQTAAEMRADLVRVHNGEPPEAPKVLTD 290
               SCOP domains d3f61a_ A: automated matches                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 3f61A01 A:1-94 Phosphorylase Kinase; domain 1                                                 -3f61A02 A:96-285 Transferase(Phosphotransferase) domain 1                                                                                                                                     ----- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee...eeeeeeeee...eeeeeeee....eeeeeeee.hhhh.hhhhhhhhhhhhh............eeeeeeeee..eeeeeeeee...eeehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhh.eeee....eee......-------------------....hhhhhhh...hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh...hhhhhh...hhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------PROTEIN_KINASE_ATP      ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (1)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f61 A   1 MTTPSHLSDRYELGEILGFGGMSEVHLARDLRDHRDVAVKVLRADLARDPSFYLRFRREAQNAAALNHPAIVAVYDTGEAETPAGPLPYIVMEYVDGVTLRDIVHTEGPMTPKRAIEVIADACQALNFSHQNGIIHRDVKPANIMISATNAVKVMDFGIA-------------------AQYLSPEQARGDSVDARSDVYSLGCVLYEVLTGEPPFTGDSPDSVAYQHVREDPIPPSARHEGLSADLDAVVLKALAKNPENRYQTAAEMRADLVRVHNGEPPEAPKVLTD 290
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160         -       180       190       200       210       220       230       240       250       260       270       280       290
                                                                                                                                                                                         160                 180                                                                                                              

Chain A from PDB  Type:PROTEIN  Length:271
 aligned with PKNB_MYCTU | P9WI81 from UniProtKB/Swiss-Prot  Length:626

    Alignment length:290
                                    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
           PKNB_MYCTU     1 MTTPSHLSDRYELGEILGFGGMSEVHLARDLRLHRDVAVKVLRADLARDPSFYLRFRREAQNAAALNHPAIVAVYDTGEAETPAGPLPYIVMEYVDGVTLRDIVHTEGPMTPKRAIEVIADACQALNFSHQNGIIHRDVKPANIMISATNAVKVMDFGIARAIADSGNSVTQTAAVIGTAQYLSPEQARGDSVDARSDVYSLGCVLYEVLTGEPPFTGDSPVSVAYQHVREDPIPPSARHEGLSADLDAVVLKALAKNPENRYQTAAEMRADLVRVHNGEPPEAPKVLTD 290
               SCOP domains d3f61a_ A: automated matches                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 3f61A01 A:1-94 Phosphorylase Kinase; domain 1                                                 -3f61A02 A:96-285 Transferase(Phosphotransferase) domain 1                                                                                                                                     ----- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee...eeeeeeeee...eeeeeeee....eeeeeeee.hhhh.hhhhhhhhhhhhh............eeeeeeeee..eeeeeeeee...eeehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhh.eeee....eee......-------------------....hhhhhhh...hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh...hhhhhh...hhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------PROTEIN_KINASE_ATP      ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f61 A   1 MTTPSHLSDRYELGEILGFGGMSEVHLARDLRDHRDVAVKVLRADLARDPSFYLRFRREAQNAAALNHPAIVAVYDTGEAETPAGPLPYIVMEYVDGVTLRDIVHTEGPMTPKRAIEVIADACQALNFSHQNGIIHRDVKPANIMISATNAVKVMDFGIA-------------------AQYLSPEQARGDSVDARSDVYSLGCVLYEVLTGEPPFTGDSPDSVAYQHVREDPIPPSARHEGLSADLDAVVLKALAKNPENRYQTAAEMRADLVRVHNGEPPEAPKVLTD 290
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160         -       180       190       200       210       220       230       240       250       260       270       280       290
                                                                                                                                                                                         160                 180                                                                                                              

   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F61)

(-) Gene Ontology  (27, 39)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PKNB_MYCTO | P9WI80)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO: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: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.

Chain A   (PKNB_MYCTU | P9WI81)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO: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:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    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:0043388    positive regulation of DNA binding    Any process that increases the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
    GO:0043085    positive regulation of catalytic activity    Any process that activates or increases the activity of an enzyme.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0051338    regulation of transferase activity    Any process that modulates the frequency, rate or extent of transferase activity, the 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:0052572    response to host immune response    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of detecting the immune response of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
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: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)

UniProtKB/Swiss-Prot
        PKNB_MYCTO | P9WI801mru 1o6y 2fum 2kud 2kue 2kuf 2kui 3f69
        PKNB_MYCTU | P9WI811mru 1o6y 2fum 2kud 2kue 2kuf 2kui 3f69 5e0y 5e0z 5e10 5e12

(-) Related Entries Specified in the PDB File

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