Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF AMINOGLYCOSIDE-3'-PHOSPHOTRANSFERASE-IIA
 
Authors :  D. Nurizzo, S. C. Shewry, E. N. Baker, C. A. Smith
Date :  06 Dec 02  (Deposition) - 16 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phosphotransferase, Protein Kinase, Atpase, Kanamycin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Nurizzo, S. C. Shewry, M. H. Perlin, S. A. Brown, J. N. Dholakia, R. L. Fuchs, T. Deva, E. N. Baker, C. A. Smith
The Crystal Structure Of Aminoglycoside-3'-Phosphotransferase-Iia, An Enzyme Responsible For Antibiotic Resistance
J. Mol. Biol. V. 327 491 2003
PubMed-ID: 12628253  |  Reference-DOI: 10.1016/S0022-2836(03)00121-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE
    Chains: A, B
    EC Number: 2.7.1.95
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: KLEBSIELLA PNEUMONIAE
    Organism Taxid: 573
    Synonym: AMINOGLYCOSIDE-3'-PHOSPHOTRANSFERASE-IIA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2KAN2Ligand/IonKANAMYCIN A
3MG2Ligand/IonMAGNESIUM ION
4NA2Ligand/IonSODIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:195 , ASP A:208 , HOH A:1615 , HOH A:1637 , HOH A:1688BINDING SITE FOR RESIDUE MG A 400
2AC2SOFTWAREPHE A:48 , GLU A:96 , VAL A:97BINDING SITE FOR RESIDUE ACT A 1500
3AC3SOFTWAREASP A:190 , CYS A:192 , KAN A:1300 , HOH A:1637BINDING SITE FOR RESIDUE NA A 1600
4AC4SOFTWAREASN B:195 , ASP B:208 , HOH B:2612 , HOH B:2697 , HOH B:2734 , HOH B:2744BINDING SITE FOR RESIDUE MG B 400
5AC5SOFTWAREPHE B:48 , VAL B:97 , MET B:197BINDING SITE FOR RESIDUE ACT B 2500
6AC6SOFTWAREASP B:190 , CYS B:192 , ASN B:195 , KAN B:2300BINDING SITE FOR RESIDUE NA B 2600
7AC7SOFTWAREASP A:157 , LEU A:158 , ASP A:159 , GLU A:160 , ASP A:190 , ARG A:211 , ARG A:226 , ASP A:227 , GLU A:230 , ASP A:261 , GLU A:262 , PHE A:264 , NA A:1600 , HOH A:1608 , HOH A:1645 , HOH A:1678 , HOH A:1688 , HOH A:1735 , HOH A:1777 , HOH A:1808BINDING SITE FOR RESIDUE KAN A 1300
8AC8SOFTWAREASP B:157 , LEU B:158 , ASP B:159 , ASP B:190 , ARG B:211 , ARG B:226 , ASP B:227 , GLU B:230 , ASP B:261 , GLU B:262 , PHE B:264 , NA B:2600 , HOH B:2609 , HOH B:2612 , HOH B:2670 , HOH B:2720BINDING SITE FOR RESIDUE KAN B 2300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ND4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ND4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ND4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ND4)

(-) Exons   (0, 0)

(no "Exon" information available for 1ND4)

(-) 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:255
 aligned with KKA2_KLEPN | P00552 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:255
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259     
           KKA2_KLEPN    10 GSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRPVLFVKTDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQDLLSSHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLDEEHQGLAPAELFARLKARMPDGEDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQDIALATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF 264
               SCOP domains d1nd4a_ A: Aminoglycoside 3'-phosphotransferase IIa (Kanamycin kinase)                                                                                                                                                                                          SCOP domains
               CATH domains 1nd4A01 A:10-95 Phosphorylase Kinase; domain 1                                        1nd4A02 A:96-264  [code=3.90.1200.10, no name defined]                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh......eeee........eeeeee......eeeeee......hhhhhhhhhhhhhh.......eeeeee....eeeeee....ee......hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh........hhhhh..hhhhhhhhhhhh......eeee....hhh.eeee..eeeee......eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nd4 A  10 GSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRPVLFVKTDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQDLLSSHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLDEEHQGLAPAELFARLKARMPDGEDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQDIALATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF 264
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259     


Chain B from PDB  Type:PROTEIN  Length:255
 aligned with KKA2_KLEPN | P00552 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:255
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259     
           KKA2_KLEPN    10 GSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRPVLFVKTDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQDLLSSHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLDEEHQGLAPAELFARLKARMPDGEDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQDIALATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF 264
               SCOP domains d1nd4b_ B: Aminoglycoside 3'-phosphotransferase IIa (Kanamycin kinase)                                                                                                                                                                                          SCOP domains
               CATH domains 1nd4B01 B:10-95 Phosphorylase Kinase; domain 1                                        1nd4B02 B:96-264  [code=3.90.1200.10, no name defined]                                                                                                                    CATH domains
           Pfam domains (1) --------------APH-1nd4B01 B:24-257                                                                                                                                                                                                                      ------- Pfam domains (1)
           Pfam domains (2) --------------APH-1nd4B02 B:24-257                                                                                                                                                                                                                      ------- Pfam domains (2)
         Sec.struct. author ..hhhhh......eeee........eeeeee......eeeeeee.....hhhhhhhhhhhhhhh......eeeeee...eeeeeee....ee......hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh........hhhhh..hhhhhhhhhhhh......eeee....hhh.eeee..eeeee......eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nd4 B  10 GSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRPVLFVKTDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQDLLSSHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLDEEHQGLAPAELFARLKARMPDGEDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQDIALATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF 264
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259
   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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PKinase (934)
(-)
Family: APH (15)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (KKA2_KLEPN | P00552)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008910    kanamycin kinase activity    Catalysis of the reaction: ATP + kanamycin = ADP + 2 H(+) + kanamycin 3'-phosphate.
    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:0016773    phosphotransferase activity, alcohol group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
    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:0046677    response to antibiotic    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 an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    KAN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1nd4)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1nd4
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  KKA2_KLEPN | P00552
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.1.95
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  KKA2_KLEPN | P00552
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1ND4)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1ND4)