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(-) Description

Title :  P4 PROTEIN FROM BACTERIOPHAGE PHI12 IN COMPLEX WITH AMPCPP
 
Authors :  E. J. Mancini, D. E. Kainov, J. M. Grimes, R. Tuma, D. H. Bamford, D. I. Stu
Date :  22 Jul 04  (Deposition) - 29 Oct 04  (Release) - 03 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
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: PSEUDOMONAS PHAGE PHI12
    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  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1APC3Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1APC6Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:133 , GLY A:135 , LYS A:136 , THR A:137 , GLU A:160 , ASN A:234 , TYR A:288 , SER A:292 , HOH A:2272 , HOH A:2273 , HOH A:2274 , HOH A:2275 , ARG C:251 , SER C:252 , GLY C:276 , GLN C:278 , LYS C:310 , HOH C:2243BINDING SITE FOR RESIDUE APC A 700
2AC2SOFTWARESER A:252 , ARG A:272 , GLY A:276 , GLN A:278 , ARG A:279 , LYS A:310 , HOH A:2225 , HOH A:2228 , GLY B:135 , LYS B:136 , THR B:137 , PRO B:138 , GLU B:160 , ASN B:234 , TYR B:288 , SER B:292 , HOH B:2144 , HOH B:2146 , HOH B:2255 , HOH B:2256 , HOH B:2257 , HOH B:2258BINDING SITE FOR RESIDUE APC B 700
3AC3SOFTWAREGLY B:276 , LEU B:277 , GLN B:278 , LYS B:310 , HOH B:2215 , GLY C:135 , LYS C:136 , THR C:137 , PRO C:138 , ASN C:234 , TYR C:288 , SER C:292 , HOH C:2138 , HOH C:2160 , HOH C:2229 , HOH C:2255 , HOH C:2256BINDING SITE FOR RESIDUE APC C 700

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1W48)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1W48)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W48)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1W48)

(-) Exons   (0, 0)

(no "Exon" information available for 1W48)

(-) 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:304
 aligned with Q94M05_9VIRU | Q94M05 from UniProtKB/TrEMBL  Length:331

    Alignment length:321
                                    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 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVIGAAGGNTTSGGISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLQRLTHTLQTSYGEHSVLTIHTSKQSGGKQASGKAIQTVIKNDEL 321
               SCOP domains d1w48a_ A: NTPase P4                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -----1w48A01 A:6-41,A:104-321            --------------------------------------------------------------1w48A01 A:6-41,A:104-321 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.....eeeeee.....eeeee....ee..eeeeeee.....eeeeeee..eeee...ee.............eeeee..eeee.eeeeee.....hhhhhhhhhhhhhhh....eeee..........hhhhhhhhhhhhhhhh.eeeee......-----------.hhhhhhhhhhhhhhhhhhh.eeeee......hhhhhhhhhhhhhhh..eeeee.....eeeeeee......eeeeeeeeee.hhh.eee...------.eehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w48 A   1 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVI-----------ISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLQRLTHTLQTSYGEHSVLTIHTS------QASGKAIQTVIKNDEL 321
                                    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        |-     | 310       320 
                                                                                                                                                                                                                            195         207                                                                                         299    306               


Chain B from PDB  Type:PROTEIN  Length:304
 aligned with Q94M05_9VIRU | Q94M05 from UniProtKB/TrEMBL  Length:331

    Alignment length:321
                                    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 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVIGAAGGNTTSGGISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLQRLTHTLQTSYGEHSVLTIHTSKQSGGKQASGKAIQTVIKNDEL 321
               SCOP domains d1w48b_ B: NTPase P4                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -----1w48B01 B:6-41,B:104-321            --------------------------------------------------------------1w48B01 B:6-41,B:104-321 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.eeeee......hhhhhhhhhhhhhhh..eeeee.....eeeeeee......eeeeeeeeee.hhh.eee...------.eehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w48 B   1 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVI-----------ISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLQRLTHTLQTSYGEHSVLTIHTS------QASGKAIQTVIKNDEL 321
                                    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        |-     | 310       320 
                                                                                                                                                                                                                            195         207                                                                                         299    306               


Chain C from PDB  Type:PROTEIN  Length:304
 aligned with Q94M05_9VIRU | Q94M05 from UniProtKB/TrEMBL  Length:331

    Alignment length:321
                                    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 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVIGAAGGNTTSGGISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLQRLTHTLQTSYGEHSVLTIHTSKQSGGKQASGKAIQTVIKNDEL 321
               SCOP domains d1w48c_ C: NTPase P4                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -----1w48C01 C:6-41,C:104-321            --------------------------------------------------------------1w48C01 C:6-41,C:104-321 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                              CATH domains
           Pfam domains (1) -NTPase_P4-1w48C01 C:2-321                                                                                                                                                                                                                                                                                                        Pfam domains (1)
           Pfam domains (2) -NTPase_P4-1w48C02 C:2-321                                                                                                                                                                                                                                                                                                        Pfam domains (2)
           Pfam domains (3) -NTPase_P4-1w48C03 C:2-321                                                                                                                                                                                                                                                                                                        Pfam domains (3)
         Sec.struct. author .....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.......eeee.....eeee.........eeeeeee.....eeeeeee..eeee...ee.............eeeee..eeee.eeeeee.....hhhhhhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhh.eeeee......-----------.hhhhhhhhhhhhhhhhhhh.eeeeee.....hhhhhhhhhhhhhhh..eeeee.....eeeeeee......eeeeeeeeee.hhh.eee...------.eehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w48 C   1 MIHLYDAKSFAKLRAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDKNAQRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVI-----------ISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLQRLTHTLQTSYGEHSVLTIHTS------QASGKAIQTVIKNDEL 321
                                    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        |-     | 310       320 
                                                                                                                                                                                                                            195         207                                                                                         299    306
   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.

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  1w48
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 Related Entries

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

UniProtKB/TrEMBL
        Q94M05_9VIRU | Q94M05: 1w44 1w46 1w47 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
1w46 P4 PROTEIN FROM BACTERIOPHAGE PHI12 IN COMPLEX WITH ADP AND MG
1w47 P4 PROTEIN FROM BACTERIOPHAGE PHI12 IN COMPLEX WITH ADP AND MN
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