Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  P4 PROTEIN FROM BACTERIOPHAGE PHI12 R279A MUTANT IN COMPLEX WITH ATP
 
Authors :  D. E. Kainov, E. J. Mancini, J. Telenius, J. Lisal, J. M. Grimes, D. H. Bamford, D. I. Stuart, R. Tuma
Date :  25 Nov 07  (Deposition) - 04 Dec 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Non-Hydrolysable Atp Analogue, Hydrolase, Virus Dsrna, Molecular Motor, Packaging Atpase, Hexameric Helicase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. E. Kainov, E. J. Mancini, J. Telenius, J. Lisal, J. M. Grimes, D. H. Bamford, D. I. Stuart, R. Tuma
Structural Basis Of Mechanochemical Coupling In A Hexameric Molecular Motor.
J. Biol. Chem. V. 283 3607 2008
PubMed-ID: 18057007  |  Reference-DOI: 10.1074/JBC.M706366200

(-) Compounds

Molecule 1 - NTPASE P4
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPG27
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector: PET 32A
    Mutation: YES
    Organism Common: BACTERIOPHAGE PHI12
    Organism Scientific: PSEUDOMONAS PHAGE PHI12
    Organism Taxid: 161736
    Synonym: P4

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1ATP3Ligand/IonADENOSINE-5'-TRIPHOSPHATE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1ATP6Ligand/IonADENOSINE-5'-TRIPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:134 , GLY A:135 , LYS A:136 , THR A:137 , ASN A:234 , TYR A:288 , SER A:292 , GLY C:276 , GLN C:278 , ASN C:318BINDING SITE FOR RESIDUE ATP A1330
2AC2SOFTWAREARG A:272 , GLY A:276 , LEU A:277 , GLN A:278 , GLY B:135 , LYS B:136 , THR B:137 , PRO B:138 , ASN B:234 , TYR B:288 , SER B:292BINDING SITE FOR RESIDUE ATP B1330
3AC3SOFTWAREARG B:272 , GLY B:276 , LEU B:277 , GLN B:278 , GLY C:135 , LYS C:136 , THR C:137 , GLU C:160 , ASN C:234 , TYR C:288 , SER C:292 , HOH C:2020BINDING SITE FOR RESIDUE ATP C1330

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VHT)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asp A:189 -Ser A:190
2Glu B:77 -Asp B:78
3Asp B:189 -Ser B:190
4Asp C:189 -Ser C:190

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VHT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VHT)

(-) Exons   (0, 0)

(no "Exon" information available for 2VHT)

(-) 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:305
 aligned with Q94M05_9VIRU | Q94M05 from UniProtKB/TrEMBL  Length:331

    Alignment length:329
                                    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         
         Q94M05_9VIRU     1 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVIGAAGGNTTSGGISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLQRLTHTLQTSYGEHSVLTIHTSKQSGGKQASGKAIQTVIKNDELESVLRRLT 329
               SCOP domains d2vhta_ A: NTPase P4                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains -----2vhtA01 A:6-41,A:104-329            --------------------------------------------------------------2vhtA01 A:6-41,A:104-329 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.......eeee.....eeee.........eeeeeee.....eeeeeee..eeee...ee.............eeeee..eeee.eeeeee.....hhhhhhhhhhhhhhh....eeee..........hhhhhhhhhhhhhhhh.eeeee.hhhhh-----------.hhhhhhhhhhhhhhhhhhh.eeeee..............hhhhhhh..eeeee.....eeeeee........eeeeeeeee.hhh.eee...-------------.ee...hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vht A   1 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVI-----------ISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLQALTHTLQTSYGEHSVLTIHTS-------------QTVIKNDELESVLRRLT 329
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    |    -      |210       220       230       240       250       260       270       280       290        |-         -  |    320         
                                                                                                                                                                                                                            195         207                                                                                         299           313                


Chain B from PDB  Type:PROTEIN  Length:305
 aligned with Q94M05_9VIRU | Q94M05 from UniProtKB/TrEMBL  Length:331

    Alignment length:329
                                    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         
         Q94M05_9VIRU     1 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVIGAAGGNTTSGGISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLQRLTHTLQTSYGEHSVLTIHTSKQSGGKQASGKAIQTVIKNDELESVLRRLT 329
               SCOP domains d2vhtb_ B: NTPase P4                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains -----2vhtB01 B:6-41,B:104-329            --------------------------------------------------------------2vhtB01 B:6-41,B:104-329 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.......eeee.....eeee.........eeeeeee.....eeeeeee..eeee...ee.............eeeee..eeee.eeeeee.....hhhhhhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhh.eeeee.hhhhh-----------.hhhhhhhhhhhhhhhhhhh.eeeee..............hhhhhhh..eeeee.....eeeeee........eeeeeeeee.hhh.eee...-------------.ee...hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vht B   1 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVI-----------ISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLQALTHTLQTSYGEHSVLTIHTS-------------QTVIKNDELESVLRRLT 329
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    |    -      |210       220       230       240       250       260       270       280       290        |-         -  |    320         
                                                                                                                                                                                                                            195         207                                                                                         299           313                


Chain C from PDB  Type:PROTEIN  Length:305
 aligned with Q94M05_9VIRU | Q94M05 from UniProtKB/TrEMBL  Length:331

    Alignment length:329
                                    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         
         Q94M05_9VIRU     1 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVIGAAGGNTTSGGISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLQRLTHTLQTSYGEHSVLTIHTSKQSGGKQASGKAIQTVIKNDELESVLRRLT 329
               SCOP domains d2vhtc_ C: NTPase P4                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains -----2vhtC01 C:6-41,C:104-329            --------------------------------------------------------------2vhtC01 C:6-41,C:104-329 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                      CATH domains
           Pfam domains (1) -NTPase_P4-2vhtC01 C:2-329                                                                                                                                                                                                                                                                                                                Pfam domains (1)
           Pfam domains (2) -NTPase_P4-2vhtC02 C:2-329                                                                                                                                                                                                                                                                                                                Pfam domains (2)
           Pfam domains (3) -NTPase_P4-2vhtC03 C:2-329                                                                                                                                                                                                                                                                                                                Pfam domains (3)
         Sec.struct. author .....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.......eeee.....eeee.........eeeeeee.....eeeeeee..eeee...ee.............eeeee..eeee.eeeeee.....hhhhhhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhh.eeeee.hhhhh-----------.hhhhhhhhhhhhhhhhhhh.eeeee..............hhhhhhh..eeeee.....eeeeee........eeeeeeeee.hhh.eee...-------------.ee...hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vht C   1 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVI-----------ISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLQALTHTLQTSYGEHSVLTIHTS-------------QTVIKNDELESVLRRLT 329
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    |    -      |210       220       230       240       250       260       270       280       290        |-         -  |    320         
                                                                                                                                                                                                                            195         207                                                                                         299           313
   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, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: NTPase_P4] (12)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q94M05_9VIRU | Q94M05)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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.

 Visualization

(-) Interactive Views

Asymmetric 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
    ATP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:189 - Ser A:190   [ RasMol ]  
    Asp B:189 - Ser B:190   [ RasMol ]  
    Asp C:189 - Ser C:190   [ RasMol ]  
    Glu B:77 - Asp B:78   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  2vht
    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
  Q94M05_9VIRU | Q94M05
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  Q94M05_9VIRU | Q94M05
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q94M05_9VIRU | Q94M05: 1w44 1w46 1w47 1w48 1w49 1w4a 1w4b 1w4c 2vhc 2vhj 2vhq 2vhu 4blr 4bls 4blt

(-) Related Entries Specified in the PDB File

1w44 P4 PROTEIN FROM BACTERIOPHAGE PHI12 IN COMPLEX WITH ADP
1w46 P4 PROTEIN FROM BACTERIOPHAGE PHI12 IN COMPLEX WITH ADP AND MG
1w47 P4 PROTEIN FROM BACTERIOPHAGE PHI12 IN COMPLEX WITH ADP AND MN
1w48 P4 PROTEIN FROM BACTERIOPHAGE PHI12 IN COMPLEX WITH AMPCPP
1w49 P4 PROTEIN FROM BACTERIOPHAGE PHI12 IN COMPLEX WITH AMPCPP AND MG
1w4a P4 PROTEIN FROM BACTERIOPHAGE PHI12 IN COMPLEX WITH AMPCPP AND MN
1w4b P4 PROTEIN FROM BACTERIOPHAGE PHI12 IN COMPLEX WITH PRODUCT (AMPCPP MG 22C)
1w4c P4 PROTEIN FROM BACTERIOPHAGE PHI12 APO STATE
2vhc P4 PROTEIN FROM BACTERIOPHAGE PHI12 N234G MUTANT IN COMPLEX WITH AMPCPP AND MN
2vhj P4 PROTEIN FROM BACTERIOPHAGE PHI12 S252A MUTANT IN COMPLEX WITH ADP
2vhq P4 PROTEIN FROM BACTERIOPHAGE PHI12 S252A MUTANT IN COMPLEX WITH ATP AND MG
2vhu P4 PROTEIN FROM BACTERIOPHAGE PHI12 K241C MUTANT IN COMPLEX WITH ADP AND MGCL