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(-) Description

Title :  P3, THE MAJOR COAT PROTEIN OF THE LIPID-CONTAINING BACTERIOPHAGE PRD1.
 
Authors :  S. D. Benson, J. K. H. Bamford, D. H. Bamford, R. M. Burnett
Date :  11 Jan 01  (Deposition) - 24 Jan 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Bacteriophage Prd1, Coat Protein, Jelly Roll, Viral Beta Barrel, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. D. Benson, J. K. Bamford, D. H. Bamford, R. M. Burnett
The X-Ray Crystal Structure Of P3, The Major Coat Protein Of The Lipid-Containing Bacteriophage Prd1, At 1. 65 A Resolution.
Acta Crystallogr. , Sect. D V. 58 39 2002
PubMed-ID: 11752778  |  Reference-DOI: 10.1107/S0907444901017279
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MAJOR CAPSID PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: SALMONELLA TYPHIMURIUM
    Expression System Strain: DS88
    Expression System Taxid: 602
    Organism Scientific: ENTEROBACTERIA PHAGE PRD1
    Organism Taxid: 10658
    Synonym: PROTEIN P3

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 27)

Asymmetric/Biological Unit (3, 27)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2MPD18Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3NA7Ligand/IonSODIUM ION

(-) Sites  (27, 27)

Asymmetric Unit (27, 27)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP B:48 , ASN B:51 , ARG B:52BINDING SITE FOR RESIDUE CL B 601
02AC2SOFTWAREASP A:48 , ASN A:51 , ARG A:52BINDING SITE FOR RESIDUE CL A 602
03AC3SOFTWAREASP B:143 , ASN B:146 , ASP B:149 , HOH B:1345 , HOH C:1139 , HOH C:1486BINDING SITE FOR RESIDUE NA B 701
04AC4SOFTWAREASN B:199 , HOH B:1007 , HOH B:1008 , HOH B:1010 , HOH B:1518 , HOH B:1519BINDING SITE FOR RESIDUE NA B 702
05AC5SOFTWAREASN A:262 , HOH A:1183 , HOH A:1184 , HOH A:1194 , HOH B:1002BINDING SITE FOR RESIDUE NA A 703
06AC6SOFTWAREASN A:199 , HOH A:1581 , HOH A:1583 , HOH A:1584 , HOH A:1585 , HOH A:1590BINDING SITE FOR RESIDUE NA A 704
07AC7SOFTWAREASP A:143 , ASN A:146 , ASP A:149 , HOH A:1124 , HOH B:1125 , HOH B:1564BINDING SITE FOR RESIDUE NA A 705
08AC8SOFTWAREGLU B:111 , GLU B:261 , HOH B:1433 , HOH B:1434 , HOH B:1435 , HOH B:1436BINDING SITE FOR RESIDUE NA B 706
09AC9SOFTWAREALA B:50 , ASN B:51 , HOH B:1014 , ASN C:51 , HOH C:1059BINDING SITE FOR RESIDUE NA C 707
10BC1SOFTWAREGLN A:107 , ARG A:108 , HIS A:109 , ASN A:259 , GLU A:261 , TYR A:282 , TYR A:379 , ALA B:81BINDING SITE FOR RESIDUE MPD A 501
11BC2SOFTWAREGLN B:327 , ARG B:330 , TRP C:167BINDING SITE FOR RESIDUE MPD B 502
12BC3SOFTWAREGLN A:327 , ARG A:330 , TRP B:167BINDING SITE FOR RESIDUE MPD A 503
13BC4SOFTWARETYR A:172 , ARG A:346 , HOH A:1395 , HOH A:1396BINDING SITE FOR RESIDUE MPD A 504
14BC5SOFTWAREASP A:105 , SER A:255 , HOH A:1198BINDING SITE FOR RESIDUE MPD A 505
15BC6SOFTWAREARG B:191 , GLU C:226 , GLU C:227BINDING SITE FOR RESIDUE MPD B 506
16BC7SOFTWAREVAL B:54 , ASP B:56 , HOH B:1411 , ASP C:48 , GLU C:227 , HOH C:1060BINDING SITE FOR RESIDUE MPD B 507
17BC8SOFTWAREVAL A:54 , ARG A:98 , LYS A:193 , GLU A:195 , ASN B:79 , ASP B:222BINDING SITE FOR RESIDUE MPD B 508
18BC9SOFTWAREGLN A:41 , TYR A:233 , ASN C:304BINDING SITE FOR RESIDUE MPD A 509
19CC1SOFTWARETYR B:172 , LEU B:285 , ARG B:346 , PRO B:349 , HOH B:1453BINDING SITE FOR RESIDUE MPD B 510
20CC2SOFTWAREASN B:262 , GLN B:277 , TYR B:284 , TYR B:377 , HOH B:1436BINDING SITE FOR RESIDUE MPD B 511
21CC3SOFTWARETYR B:305 , LYS B:318 , GLN C:41 , TYR C:233BINDING SITE FOR RESIDUE MPD C 512
22CC4SOFTWAREASP B:105 , SER B:255 , ARG B:383 , HOH B:1555BINDING SITE FOR RESIDUE MPD B 513
23CC5SOFTWARETHR A:73 , GLU A:161 , GLU A:227 , SER A:229 , ASN C:106 , ARG C:191BINDING SITE FOR RESIDUE MPD C 514
24CC6SOFTWAREASP C:105 , LEU C:251 , LEU C:254 , ARG C:383BINDING SITE FOR RESIDUE MPD C 515
25CC7SOFTWARELYS C:124 , TYR C:172 , HOH C:1233BINDING SITE FOR RESIDUE MPD C 516
26CC8SOFTWARETYR C:172 , LEU C:285 , ARG C:346 , PRO C:349 , PHE C:380 , HOH C:1237BINDING SITE FOR RESIDUE MPD C 517
27CC9SOFTWARETRP A:167 , GLN C:327 , ARG C:330BINDING SITE FOR RESIDUE MPD C 518

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1HX6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1HX6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1HX6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1HX6)

(-) Exons   (0, 0)

(no "Exon" information available for 1HX6)

(-) 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:370
 aligned with CAPSD_BPPRD | P22535 from UniProtKB/Swiss-Prot  Length:395

    Alignment length:370
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384
          CAPSD_BPPRD    15 LRNQQAMAANLQARQIVLQQSYPVIQQVETQTFDPANRSVFDVTPANVGIVKGFLVKVTAAITNNHATEAVALTDFGPANLVQRVIYYDPDNQRHTETSGWHLHFVNTAKQGAPFLSSMVTDSPIKYGDVMNVIDAPATIAAGATGELTMYYWVPLAYSETDLTGAVLANVPQSKQRLKLEFANNNTAFAAVGANPLEAIYQGAGAADCEFEEISYTVYQSYLDQLPVGQNGYILPLIDLSTLYNLENSAQAGLTPNVDFVVQYANLYRYLSTIAVFDNGGSFNAGTDINYLSQRTANFSDTRKLDPKTWAAQTRRRIATDFPKGVYYCDNRDKPIYTLQYGNVGFVVNPKTVNQNARLLMGYEYFTSRT 384
               SCOP domains d1hx6a1 A:15-244 Coat protein p3                                                                                                                                                                                                      d1hx6a2 A:245-384 Coat protein p3                                                                                                            SCOP domains
               CATH domains 1hx6A01 A:15-243 Viral coat protein p3                                                                                                                                                                                               1hx6A02 A:244-384  [code=2.60.120.20, no name defined]                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhheeeeeeeeeeee......eeee......eeeeeeeeeeeeeee......eee..hhhhh.eeeeeee.....eeeeeehhhhhhhhhhhhh..........................ee....eeeeeeeeeee...........ee........eeeeee......ee..........ee..hhh.eeeeeeeeeeeeeeee...........hhhhhheeeeeeeeeee.......eeee.....eeeeeeeeeee.........eeeeeeee...ee....hhhhhhhhhhhhhh......eeeee.............eeeeeee......eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hx6 A  15 LRNQQAMAANLQARQIVLQQSYPVIQQVETQTFDPANRSVFDVTPANVGIVKGFLVKVTAAITNNHATEAVALTDFGPANLVQRVIYYDPDNQRHTETSGWHLHFVNTAKQGAPFLSSMVTDSPIKYGDVMNVIDAPATIAAGATGELTMYYWVPLAYSETDLTGAVLANVPQSKQRLKLEFANNNTAFAAVGANPLEAIYQGAGAADCEFEEISYTVYQSYLDQLPVGQNGYILPLIDLSTLYNLENSAQAGLTPNVDFVVQYANLYRYLSTIAVFDNGGSFNAGTDINYLSQRTANFSDTRKLDPKTWAAQTRRRIATDFPKGVYYCDNRDKPIYTLQYGNVGFVVNPKTVNQNARLLMGYEYFTSRT 384
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384


Chain B from PDB  Type:PROTEIN  Length:374
 aligned with CAPSD_BPPRD | P22535 from UniProtKB/Swiss-Prot  Length:395

    Alignment length:374
                                    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       330       340       350       360       370       380    
          CAPSD_BPPRD    11 QQAALRNQQAMAANLQARQIVLQQSYPVIQQVETQTFDPANRSVFDVTPANVGIVKGFLVKVTAAITNNHATEAVALTDFGPANLVQRVIYYDPDNQRHTETSGWHLHFVNTAKQGAPFLSSMVTDSPIKYGDVMNVIDAPATIAAGATGELTMYYWVPLAYSETDLTGAVLANVPQSKQRLKLEFANNNTAFAAVGANPLEAIYQGAGAADCEFEEISYTVYQSYLDQLPVGQNGYILPLIDLSTLYNLENSAQAGLTPNVDFVVQYANLYRYLSTIAVFDNGGSFNAGTDINYLSQRTANFSDTRKLDPKTWAAQTRRRIATDFPKGVYYCDNRDKPIYTLQYGNVGFVVNPKTVNQNARLLMGYEYFTSRT 384
               SCOP domains d1hx6b1 B:11-244 Coat protein p3                                                                                                                                                                                                          d1hx6b2 B:245-384 Coat protein p3                                                                                                            SCOP domains
               CATH domains 1hx6B01 B:11-243 Viral coat protein p3                                                                                                                                                                                                   1hx6B02 B:244-384  [code=2.60.120.20, no name defined]                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhheeeeeeeeeeee......eeee......eeeeeeeeeeeeeee......eee..hhhhh.eeeeeee.....eeeeeehhhhhhhhhhhhh..........................ee....eeeeeeeeeee...........ee........eeeeee......ee..........ee..hhh.eeeeeeeeeeeeeeee...ee..ee....hhh.eeeeeeeeee........eeee.....eeeeeeeeeee.........eeeeeeee.........hhhhhhhhhhhhhh......eeeee.............eeeeeee......eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hx6 B  11 QQAALRNQQAMAANLQARQIVLQQSYPVIQQVETQTFDPANRSVFDVTPANVGIVKGFLVKVTAAITNNHATEAVALTDFGPANLVQRVIYYDPDNQRHTETSGWHLHFVNTAKQGAPFLSSMVTDSPIKYGDVMNVIDAPATIAAGATGELTMYYWVPLAYSETDLTGAVLANVPQSKQRLKLEFANNNTAFAAVGANPLEAIYQGAGAADCEFEEISYTVYQSYLDQLPVGQNGYILPLIDLSTLYNLENSAQAGLTPNVDFVVQYANLYRYLSTIAVFDNGGSFNAGTDINYLSQRTANFSDTRKLDPKTWAAQTRRRIATDFPKGVYYCDNRDKPIYTLQYGNVGFVVNPKTVNQNARLLMGYEYFTSRT 384
                                    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       330       340       350       360       370       380    


Chain C from PDB  Type:PROTEIN  Length:371
 aligned with CAPSD_BPPRD | P22535 from UniProtKB/Swiss-Prot  Length:395

    Alignment length:371
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383 
          CAPSD_BPPRD    14 ALRNQQAMAANLQARQIVLQQSYPVIQQVETQTFDPANRSVFDVTPANVGIVKGFLVKVTAAITNNHATEAVALTDFGPANLVQRVIYYDPDNQRHTETSGWHLHFVNTAKQGAPFLSSMVTDSPIKYGDVMNVIDAPATIAAGATGELTMYYWVPLAYSETDLTGAVLANVPQSKQRLKLEFANNNTAFAAVGANPLEAIYQGAGAADCEFEEISYTVYQSYLDQLPVGQNGYILPLIDLSTLYNLENSAQAGLTPNVDFVVQYANLYRYLSTIAVFDNGGSFNAGTDINYLSQRTANFSDTRKLDPKTWAAQTRRRIATDFPKGVYYCDNRDKPIYTLQYGNVGFVVNPKTVNQNARLLMGYEYFTSRT 384
               SCOP domains d1hx6c1 C:14-244 Coat protein p3                                                                                                                                                                                                       d1hx6c2 C:245-384 Coat protein p3                                                                                                            SCOP domains
               CATH domains 1hx6C01 C:14-243 Viral coat protein p3                                                                                                                                                                                                1hx6C02 C:244-384  [code=2.60.120.20, no name defined]                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhheeeeeeeeeeee......eeee......eeeeeeeeeeeeeee......eee..hhhhh.eeeeeee.....eeeeeehhhhhhhhhhhhh..........................ee....eeeeeeeeeee...........ee........eeeeee.hhhhhee..........ee..hhh.eeeeeeeeeeeeeeee...ee..ee..hhhhhheeeeeeeeeee.......eeee.....eeeeeeeeeee.........eeeeeeee.........hhhhhhhhhhhhhh......eeeee.............eeeeeee......eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hx6 C  14 ALRNQQAMAANLQARQIVLQQSYPVIQQVETQTFDPANRSVFDVTPANVGIVKGFLVKVTAAITNNHATEAVALTDFGPANLVQRVIYYDPDNQRHTETSGWHLHFVNTAKQGAPFLSSMVTDSPIKYGDVMNVIDAPATIAAGATGELTMYYWVPLAYSETDLTGAVLANVPQSKQRLKLEFANNNTAFAAVGANPLEAIYQGAGAADCEFEEISYTVYQSYLDQLPVGQNGYILPLIDLSTLYNLENSAQAGLTPNVDFVVQYANLYRYLSTIAVFDNGGSFNAGTDINYLSQRTANFSDTRKLDPKTWAAQTRRRIATDFPKGVYYCDNRDKPIYTLQYGNVGFVVNPKTVNQNARLLMGYEYFTSRT 384
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HX6)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (CAPSD_BPPRD | P22535)
molecular function
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
cellular component
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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  1hx6
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  CAPSD_BPPRD | P22535
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 Related Entries

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

UniProtKB/Swiss-Prot
        CAPSD_BPPRD | P22535: 1cjd 1gw7 1gw8 1hb5 1hb7 1hb9 1hqn 1w8x

(-) Related Entries Specified in the PDB File

1cjd 1CJD IS P3 AT 1.85 RESOLUTION
1hqn 1HQN IS SELENOMETHIONINE DERIVATIVE OF P3