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(-) Description

Title :  P4 PROTEIN FROM BACTERIOPHAGE PHI12 IN COMPLEX WITH ADP AND MG
 
Authors :  E. J. Mancini, D. E. Kainov, J. M. Grimes, R. Tuma, D. H. Bamford, D. I. Stuart
Date :  22 Jul 04  (Deposition) - 04 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Dsrna Virus, Packaging Atpase, Hexameric Helicase, Molecular Motor, Non-Hydrolysable Atp Analogue, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. J. Mancini, D. E. Kainov, J. M. Grimes, R. Tuma, D. H. Bamford, D. I. Stuart
Atomic Snapshots Of An Rna Packaging Motor Reveal Conformational Changes Linking Atp Hydrolysis To Rna Translocation
Cell(Cambridge, Mass. ) V. 118 743 2004
PubMed-ID: 15369673  |  Reference-DOI: 10.1016/J.CELL.2004.09.007

(-) 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
    Organism Common: BACTERIOPHAGE PHI12
    Organism Scientific: BACTERIOPHAGE PHI-12
    Organism Taxid: 161736
    Synonym: P4 PACKAGING ATPASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1ADP3Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG3Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1ADP6Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:137 , ASP A:189 , SER A:232 , ADP A:700BINDING SITE FOR RESIDUE MG A 701
2AC2SOFTWARETHR B:137 , ASP B:189 , SER B:232 , ADP B:700BINDING SITE FOR RESIDUE MG B 701
3AC3SOFTWARETHR C:137 , ASP C:189 , SER C:232 , ADP C:700BINDING SITE FOR RESIDUE MG C 701
4AC4SOFTWAREASN A:133 , SER A:134 , GLY A:135 , LYS A:136 , THR A:137 , ASN A:234 , TYR A:288 , SER A:292 , MG A:701 , HOH A:2103 , HOH A:2111 , GLY C:276 , LEU C:277 , ARG C:279BINDING SITE FOR RESIDUE ADP A 700
5AC5SOFTWAREGLY A:276 , LEU A:277 , ARG A:279 , ASN B:133 , SER B:134 , GLY B:135 , LYS B:136 , THR B:137 , ASN B:234 , TYR B:288 , SER B:292 , MG B:701BINDING SITE FOR RESIDUE ADP B 700
6AC6SOFTWAREGLY B:276 , LEU B:277 , ARG B:279 , ASN C:133 , SER C:134 , GLY C:135 , LYS C:136 , THR C:137 , ASN C:234 , TYR C:288 , SER C:292 , MG C:701 , HOH C:2100 , HOH C:2108 , HOH C:2109BINDING SITE FOR RESIDUE ADP C 700

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1W46)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1W46)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W46)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1W46)

(-) Exons   (0, 0)

(no "Exon" information available for 1W46)

(-) 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:288
 aligned with Q94M05_9VIRU | Q94M05 from UniProtKB/TrEMBL  Length:331

    Alignment length:299
                                    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         
         Q94M05_9VIRU     1 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVIGAAGGNTTSGGISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLQRLTHTLQTSYGEHSVLTIHTS 299
               SCOP domains d1w46a_ A: NTPase P4                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1w46A01 A:1-41,A:104-299                 --------------------------------------------------------------1w46A01 A:1-41,A:104-299 P-loop containing nucleotide triphosphate hydrolases                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.......eeee.....eeee.....ee..eeeeeee.....eeeeeee..eeee...ee.............eeeee..eeee.eeeeee.....hhhhhhhhhhhhhhh....eeee..........hhhhhhhhhhhhhhhh.eeeee......-----------.hhhhhhhhhhhhhhhhhhh.eeeeee.......hhhhhhhhhhhhhh.eeeee.....eeeeeee......eeeeeeeeee.hhh.eee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w46 A   1 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVI-----------ISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLQRLTHTLQTSYGEHSVLTIHTS 299
                                    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         
                                                                                                                                                                                                                            195         207                                                                                            


Chain B from PDB  Type:PROTEIN  Length:288
 aligned with Q94M05_9VIRU | Q94M05 from UniProtKB/TrEMBL  Length:331

    Alignment length:299
                                    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         
         Q94M05_9VIRU     1 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVIGAAGGNTTSGGISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLQRLTHTLQTSYGEHSVLTIHTS 299
               SCOP domains d1w46b_ B: NTPase P4                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1w46B01 B:1-41,B:104-299                 --------------------------------------------------------------1w46B01 B:1-41,B:104-299 P-loop containing nucleotide triphosphate hydrolases                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.......eeee.....eeee.....ee..eeeeeee.....eeeeeee..eeee...ee.............eeeee..eeee.eeeeee.....hhhhhhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhh.eeeee......-----------.hhhhhhhhhhhhhhhhhhh.eeeeee.......hhhhhhhhhhhhhh.eeeee.....eeeeeee......eeeeeeeeee.hhh.eee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w46 B   1 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVI-----------ISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLQRLTHTLQTSYGEHSVLTIHTS 299
                                    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         
                                                                                                                                                                                                                            195         207                                                                                            


Chain C from PDB  Type:PROTEIN  Length:288
 aligned with Q94M05_9VIRU | Q94M05 from UniProtKB/TrEMBL  Length:331

    Alignment length:299
                                    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         
         Q94M05_9VIRU     1 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVIGAAGGNTTSGGISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLQRLTHTLQTSYGEHSVLTIHTS 299
               SCOP domains d1w46c_ C: NTPase P4                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1w46C01 C:1-41,C:104-299                 --------------------------------------------------------------1w46C01 C:1-41,C:104-299 P-loop containing nucleotide triphosphate hydrolases                                                                                                                        CATH domains
           Pfam domains (1) -NTPase_P4-1w46C01 C:2-299                                                                                                                                                                                                                                                                                  Pfam domains (1)
           Pfam domains (2) -NTPase_P4-1w46C02 C:2-299                                                                                                                                                                                                                                                                                  Pfam domains (2)
           Pfam domains (3) -NTPase_P4-1w46C03 C:2-299                                                                                                                                                                                                                                                                                  Pfam domains (3)
         Sec.struct. author .....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......eeee.....eeee.....ee..eeeeeee.....eeeeeee..eeee...ee.............eeeee..eeee.eeeeee.....hhhhhhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhh.eeeee......-----------.hhhhhhhhhhhhhhhhhhh.eeeeee.......hhhhhhhhhhhhhh.eeeee.....eeeeeee......eeeeeeeeee.hhh.eee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w46 C   1 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVI-----------ISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLQRLTHTLQTSYGEHSVLTIHTS 299
                                    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         
                                                                                                                                                                                                                            195         207
   Legend:   → Mismatch (orange background)
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  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.

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  1w46
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1w44 P4 PROTEIN FROM BACTERIOPHAGE PHI12 IN COMPLEX WITH ADP
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