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(-) Description

Title :  CRYSTAL STRUCTURE OF THE STIV MCP
 
Authors :  R. Khayat
Date :  17 Oct 05  (Deposition) - 06 Dec 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Archaea, Hyperthermophile, Virus, Evolution, Crystal, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Khayat, L. Tang, E. T. Larson, C. M. Lawrence, M. Young, J. E. Johnson
Structure Of An Archaeal Virus Capsid Protein Reveals A Common Ancestry To Eukaryotic And Bacterial Viruses.
Proc. Natl. Acad. Sci. Usa V. 102 18944 2005
PubMed-ID: 16357204  |  Reference-DOI: 10.1073/PNAS.0506383102

(-) Compounds

Molecule 1 - COAT PROTEIN
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificSULFOLOBUS TURRETED ICOSAHEDRAL VIRUS
    Organism Taxid269145

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 33)

Asymmetric Unit (2, 33)
No.NameCountTypeFull Name
1MPD17Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1MPD8Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (2, 9)
No.NameCountTypeFull Name
1MPD5Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (2, 7)
No.NameCountTypeFull Name
1MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:79 , THR A:81 , GLU A:188 , TYR A:218 , TYR A:307 , HOH A:1068 , HOH A:1101 , HOH B:1050BINDING SITE FOR RESIDUE MPD A 1001
02AC2SOFTWAREASP A:120 , PRO A:184 , LYS A:213 , SER A:312BINDING SITE FOR RESIDUE MPD A 1002
03AC3SOFTWARELEU A:166 , GLY A:169 , HOH A:1056 , GLY B:172 , ALA B:173BINDING SITE FOR RESIDUE MPD A 1003
04AC4SOFTWAREPHE A:192 , MPD A:1005 , SER B:79 , THR B:81 , TYR B:218 , TYR B:307 , HOH B:1011 , HOH B:1151BINDING SITE FOR RESIDUE MPD A 1004
05AC5SOFTWAREASN A:193 , ASN A:305 , MPD A:1004 , PRO B:56 , HOH B:1042 , HOH B:1151BINDING SITE FOR RESIDUE MPD A 1005
06AC6SOFTWARETYR A:88 , PRO A:101 , PRO A:266 , TYR A:267 , HOH A:1102 , HOH A:1117BINDING SITE FOR RESIDUE MPD A 1006
07AC7SOFTWAREALA C:196 , SER C:197 , SER C:198 , LEU C:300 , GLN C:301BINDING SITE FOR RESIDUE MPD C 1007
08AC8SOFTWAREGLN C:207 , PRO C:208 , SER C:291 , ASP C:292 , HOH C:1119 , ASN D:20BINDING SITE FOR RESIDUE MPD C 1008
09AC9SOFTWARELYS A:24 , ARG A:27 , ASN A:28 , HOH A:1024 , HOH A:1264BINDING SITE FOR RESIDUE MPD A 1009
10BC1SOFTWAREARG B:27 , ASN B:131BINDING SITE FOR RESIDUE MPD B 1010
11BC2SOFTWAREARG C:27 , ASN C:131BINDING SITE FOR RESIDUE MPD C 1011
12BC3SOFTWAREASP C:120 , PRO C:184 , LYS C:213 , SER C:312BINDING SITE FOR RESIDUE MPD C 1012
13BC4SOFTWARESER C:79 , THR C:81 , TYR C:218 , TYR C:307 , HOH C:1024BINDING SITE FOR RESIDUE MPD C 1013
14BC5SOFTWAREGLU A:3 , TYR A:5 , GLU D:3 , TYR D:5BINDING SITE FOR RESIDUE MPD A 1014
15BC6SOFTWAREPHE C:192 , SER D:79 , THR D:81 , TYR D:218 , ILE D:220 , TYR D:307 , MPD D:1017 , HOH D:1050BINDING SITE FOR RESIDUE MPD D 1015
16BC7SOFTWARETYR D:88 , PRO D:266 , TYR D:267 , HOH D:1136BINDING SITE FOR RESIDUE MPD D 1016
17BC8SOFTWAREASN C:193 , ASN C:305 , PRO D:56 , MPD D:1015 , HOH D:1079BINDING SITE FOR RESIDUE MPD D 1017

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Ala A:55 -Pro A:56
2Phe A:57 -Pro A:58
3Tyr A:98 -Pro A:99
4Ala B:55 -Pro B:56
5Phe B:57 -Pro B:58
6Tyr B:98 -Pro B:99
7Ala C:55 -Pro C:56
8Phe C:57 -Pro C:58
9Tyr C:98 -Pro C:99
10Ala D:55 -Pro D:56
11Phe D:57 -Pro D:58
12Tyr D:98 -Pro D:99

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2BBD)

(-) 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:323
 aligned with Q6Q0J0_9VIRU | Q6Q0J0 from UniProtKB/TrEMBL  Length:345

    Alignment length:323
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321   
         Q6Q0J0_9VIRU     2 GEIYTETLQQTYAWTAGTNIPIKIPRNNFIRKIRVQLIGSISNSGTAAVTLPSAPFPYNLVQTFNLSYEGSKTLYSVSGTGLGILMYYTTKGQNPAYPAPGTSVPASGSVNLNVMWEFDLARFPATMVQNIILSILTGQAPSGVSINASFYITITYERVTAQEILSEGGLGADGEMPLATVLPKVIEIPTFNVPASSAPIHVAYLQPGQIYKRQLVYVINSTSGINNTDPTEYELKIVRGVPTDKIKVSWAALQAENQAEYQVAPYSGASAIIDFRKYFNGDLDLTHAPSDSIEYDLALQNQDNVYSLYVSYVLPYYDQLAAL 324
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....ee.....eeeeee....eeeeeeeeeeeeeee.....ee......hhh.eeeeeeee...eeeeeeehhhhhhhhhhhh.....ee.....ee...eeeeeeeeeeeeeeeehhhhh..eeeeeee.......eeeeeeeeeeeeee.hhhhhhhh..............eeeeeeeeeeee......eeeee.....eeeeeeeeee..........eeeeeeee.....eeeeeeehhhhhhhhhhhhh.......eeeee.hhh....ee........eeeeeee...eeeeeeeeeee..hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bbd A   2 GEIYTETLQQTYAWTAGTNIPIKIPRNNFIRKIRVQLIGSISNSGTAAVTLPSAPFPYNLVQTFNLSYEGSKTLYSVSGTGLGILmYYTTKGQNPAYPAPGTSVPASGSVNLNVmWEFDLARFPATmVQNIILSILTGQAPSGVSINASFYITITYERVTAQEILSEGGLGADGEmPLATVLPKVIEIPTFNVPASSAPIHVAYLQPGQIYKRQLVYVINSTSGINNTDPTEYELKIVRGVPTDKIKVSWAALQAENQAEYQVAPYSGASAIIDFRKYFNGDLDLTHAPSDSIEYDLALQNQDNVYSLYVSYVLPYYDQLAAL 324
                                    11        21        31        41        51        61        71        81     |  91       101       111    |  121      |131       141       151       161       171     | 181       191       201       211       221       231       241       251       261       271       281       291       301       311       321   
                                                                                                                87-MSE                      116-MSE     128-MSE                                          177-MSE                                                                                                                                               

Chain B from PDB  Type:PROTEIN  Length:323
 aligned with Q6Q0J0_9VIRU | Q6Q0J0 from UniProtKB/TrEMBL  Length:345

    Alignment length:323
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321   
         Q6Q0J0_9VIRU     2 GEIYTETLQQTYAWTAGTNIPIKIPRNNFIRKIRVQLIGSISNSGTAAVTLPSAPFPYNLVQTFNLSYEGSKTLYSVSGTGLGILMYYTTKGQNPAYPAPGTSVPASGSVNLNVMWEFDLARFPATMVQNIILSILTGQAPSGVSINASFYITITYERVTAQEILSEGGLGADGEMPLATVLPKVIEIPTFNVPASSAPIHVAYLQPGQIYKRQLVYVINSTSGINNTDPTEYELKIVRGVPTDKIKVSWAALQAENQAEYQVAPYSGASAIIDFRKYFNGDLDLTHAPSDSIEYDLALQNQDNVYSLYVSYVLPYYDQLAAL 324
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....ee.....eeeeee....eeeeeeeeeeeeeee.....ee......hhh.eeeeeeee...eeeeeeehhhhhhhhhhhh.....ee.....ee...eeeeeeeeeeeeeeeehhhhh..eeeeeee.......eeeeeeeeeeeeee.hhhhhhhh..............eeeeeeeeeeee......eeeee.....eeeeeeeeee..........eeeeeeee........eeeehhhhhhhhhhhhh.......eeeee.hhh....ee........eeeeeee...eeeeeeeeeee..hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bbd B   2 GEIYTETLQQTYAWTAGTNIPIKIPRNNFIRKIRVQLIGSISNSGTAAVTLPSAPFPYNLVQTFNLSYEGSKTLYSVSGTGLGILmYYTTKGQNPAYPAPGTSVPASGSVNLNVmWEFDLARFPATmVQNIILSILTGQAPSGVSINASFYITITYERVTAQEILSEGGLGADGEmPLATVLPKVIEIPTFNVPASSAPIHVAYLQPGQIYKRQLVYVINSTSGINNTDPTEYELKIVRGVPTDKIKVSWAALQAENQAEYQVAPYSGASAIIDFRKYFNGDLDLTHAPSDSIEYDLALQNQDNVYSLYVSYVLPYYDQLAAL 324
                                    11        21        31        41        51        61        71        81     |  91       101       111    |  121      |131       141       151       161       171     | 181       191       201       211       221       231       241       251       261       271       281       291       301       311       321   
                                                                                                                87-MSE                      116-MSE     128-MSE                                          177-MSE                                                                                                                                               

Chain C from PDB  Type:PROTEIN  Length:323
 aligned with Q6Q0J0_9VIRU | Q6Q0J0 from UniProtKB/TrEMBL  Length:345

    Alignment length:323
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321   
         Q6Q0J0_9VIRU     2 GEIYTETLQQTYAWTAGTNIPIKIPRNNFIRKIRVQLIGSISNSGTAAVTLPSAPFPYNLVQTFNLSYEGSKTLYSVSGTGLGILMYYTTKGQNPAYPAPGTSVPASGSVNLNVMWEFDLARFPATMVQNIILSILTGQAPSGVSINASFYITITYERVTAQEILSEGGLGADGEMPLATVLPKVIEIPTFNVPASSAPIHVAYLQPGQIYKRQLVYVINSTSGINNTDPTEYELKIVRGVPTDKIKVSWAALQAENQAEYQVAPYSGASAIIDFRKYFNGDLDLTHAPSDSIEYDLALQNQDNVYSLYVSYVLPYYDQLAAL 324
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee.....eeeeee....eeeeeeeeeeeeeee.....ee......hhh.eeeeeeee...eeeeeeehhhhhhhhhhhh.....ee.....ee...eeeeeeeeeeeeeeeehhhhh..eeeeeee.......eeeeeeeeeeeee..hhhhhhh...............eeeeeeeeeeee......eeeee.....eeeeeeeeee..........eeeeeeee.....eeeeeeehhhhhhhhhhhhh.......eeeee.hhh....ee........eeeeeee...eeeeeeeeeee..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bbd C   2 GEIYTETLQQTYAWTAGTNIPIKIPRNNFIRKIRVQLIGSISNSGTAAVTLPSAPFPYNLVQTFNLSYEGSKTLYSVSGTGLGILmYYTTKGQNPAYPAPGTSVPASGSVNLNVmWEFDLARFPATmVQNIILSILTGQAPSGVSINASFYITITYERVTAQEILSEGGLGADGEmPLATVLPKVIEIPTFNVPASSAPIHVAYLQPGQIYKRQLVYVINSTSGINNTDPTEYELKIVRGVPTDKIKVSWAALQAENQAEYQVAPYSGASAIIDFRKYFNGDLDLTHAPSDSIEYDLALQNQDNVYSLYVSYVLPYYDQLAAL 324
                                    11        21        31        41        51        61        71        81     |  91       101       111    |  121      |131       141       151       161       171     | 181       191       201       211       221       231       241       251       261       271       281       291       301       311       321   
                                                                                                                87-MSE                      116-MSE     128-MSE                                          177-MSE                                                                                                                                               

Chain D from PDB  Type:PROTEIN  Length:323
 aligned with Q6Q0J0_9VIRU | Q6Q0J0 from UniProtKB/TrEMBL  Length:345

    Alignment length:323
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321   
         Q6Q0J0_9VIRU     2 GEIYTETLQQTYAWTAGTNIPIKIPRNNFIRKIRVQLIGSISNSGTAAVTLPSAPFPYNLVQTFNLSYEGSKTLYSVSGTGLGILMYYTTKGQNPAYPAPGTSVPASGSVNLNVMWEFDLARFPATMVQNIILSILTGQAPSGVSINASFYITITYERVTAQEILSEGGLGADGEMPLATVLPKVIEIPTFNVPASSAPIHVAYLQPGQIYKRQLVYVINSTSGINNTDPTEYELKIVRGVPTDKIKVSWAALQAENQAEYQVAPYSGASAIIDFRKYFNGDLDLTHAPSDSIEYDLALQNQDNVYSLYVSYVLPYYDQLAAL 324
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....ee.....eeeee.....eeeeeeeeeeeeeee.....ee......hhh.eeeeeeee...eeeeeeehhhhhhhhhhhh.....ee.....ee...eeeeeeeeeeeeeeeehhhhh...eeeeee.......eeeeeeeeeeeeee.hhhhhhhh..............eeeeeeeeeeee..eeeeeeeee.....eeeeeeeeee..........eeeeeeee.....eeeeeeehhhhhhhhhhhhh.......eeeee.hhh....ee........eeeeeee...eeeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bbd D   2 GEIYTETLQQTYAWTAGTNIPIKIPRNNFIRKIRVQLIGSISNSGTAAVTLPSAPFPYNLVQTFNLSYEGSKTLYSVSGTGLGILmYYTTKGQNPAYPAPGTSVPASGSVNLNVmWEFDLARFPATmVQNIILSILTGQAPSGVSINASFYITITYERVTAQEILSEGGLGADGEmPLATVLPKVIEIPTFNVPASSAPIHVAYLQPGQIYKRQLVYVINSTSGINNTDPTEYELKIVRGVPTDKIKVSWAALQAENQAEYQVAPYSGASAIIDFRKYFNGDLDLTHAPSDSIEYDLALQNQDNVYSLYVSYVLPYYDQLAAL 324
                                    11        21        31        41        51        61        71        81     |  91       101       111    |  121      |131       141       151       161       171     | 181       191       201       211       221       231       241       251       261       271       281       291       301       311       321   
                                                                                                                87-MSE                      116-MSE     128-MSE                                          177-MSE                                                                                                                                               

   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  (0, 0)

(no "SCOP Domain" information available for 2BBD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2BBD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BBD)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q6Q0J0_9VIRU | Q6Q0J0)
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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(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        Q6Q0J0_9VIRU | Q6Q0J03j31

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