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(-) Description

Title :  CRYSTAL STRUCTURE OF SERYL-TRNA SYNTHETASE FROM HUMAN AT 2.9 ANGSTROMS
 
Authors :  X. L. Xu, X. -L. Yang
Date :  02 Jan 12  (Deposition) - 29 Feb 12  (Release) - 21 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.89
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Coiled-Coil, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Xu, Y. Shi, H. M. Zhang, E. C. Swindell, A. G. Marshall, M. Guo, S. Kishi, X. L. Yang
Unique Domain Appended To Vertebrate Trna Synthetase Is Essential For Vascular Development.
Nat Commun V. 3 681 2012
PubMed-ID: 22353712  |  Reference-DOI: 10.1038/NCOMMS1686

(-) Compounds

Molecule 1 - SERYL-TRNA SYNTHETASE, CYTOPLASMIC
    ChainsA, B, C, D, E, F
    EC Number6.1.1.11
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET20B
    Expression System StrainE.COLI BL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneSARS, SERS
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSERINE--TRNA LIGASE, SERRS, SERYL-TRNA(SER/SEC) SYNTHETASE

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)AB    
Biological Unit 2 (1x)  CD  
Biological Unit 3 (1x)    EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2PO46Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:302 , PHE A:316 , PHE A:321BINDING SITE FOR RESIDUE MG A 601
2AC2SOFTWARETHR A:312 , GLY A:314 , ARG A:317BINDING SITE FOR RESIDUE PO4 A 602
3AC3SOFTWAREGLU B:391BINDING SITE FOR RESIDUE MG B 601
4AC4SOFTWAREARG B:192 , GLY B:309 , THR B:312 , ARG B:317BINDING SITE FOR RESIDUE PO4 B 602
5AC5SOFTWARETHR C:312 , ARG C:313BINDING SITE FOR RESIDUE PO4 C 601
6AC6SOFTWARETHR D:312 , GLY D:314 , ARG D:317BINDING SITE FOR RESIDUE PO4 D 601
7AC7SOFTWAREARG E:313 , ARG E:317BINDING SITE FOR RESIDUE PO4 E 601
8AC8SOFTWAREHIS F:170 , ARG F:317BINDING SITE FOR RESIDUE PO4 F 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VBB)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Leu A:290 -Pro A:291
2Leu B:290 -Pro B:291
3Leu C:290 -Pro C:291
4Leu D:290 -Pro D:291
5Leu E:290 -Pro E:291
6Leu F:290 -Pro F:291

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 6)

Asymmetric Unit (1, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_078434D172NSYSC_HUMANDisease  ---A/B/C/D/E/FD172N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_078434D172NSYSC_HUMANDisease  ---A/BD172N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_078434D172NSYSC_HUMANDisease  ---C/DD172N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_078434D172NSYSC_HUMANDisease  ---E/FD172N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VBB)

(-) Exons   (0, 0)

(no "Exon" information available for 3VBB)

(-) 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:451
 aligned with SYSC_HUMAN | P49591 from UniProtKB/Swiss-Prot  Length:514

    Alignment length:475
                                    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       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471     
           SYSC_HUMAN     2 VLDLDLFRVDKGGDPALIRETQEKRFKDPGLVDQLVKADSEWRRCRFRADNLNKLKNLCSKTIGEKMKKKEPVGDDESVPENVLSFDDLTADALANLKVSQIKKVRLLIDEAILKCDAERIKLEAERFENLREIGNLLHPSVPISNDEDVDNKVERIWGDCTVRKKYSHVDLVVMVDGFEGEKGAVVAGSRGYFLKGVLVFLEQALIQYALRTLGSRGYIPIYTPFFMRKEVMQEVAQLSQFDEELYKVIGKGSEKSDDNSYDEKYLIATSEQPIAALHRDEWLRPEDLPIKYAGLSTCFRQEVGSHGRDTRGIFRVHQFEKIEQFVYSSPHDNKSWEMFEEMITTAEEFYQSLGIPYHIVNIVSGSLNHAASKKLDLEAWFPGSGAFRELVSCSNCTDYQARRLRIRYGQTKKMMDKVEFVHMLNATMCATTRTICAILENYQTEKGITVPEKLKEFMPPGLQELIPFVKPAPI 476
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.----....hhhhh.....hhhhhhh....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh............hhhhhheeeeee.........hhhhhhhhh..eehhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhh..eeee...eeehhhhhhhh...-......eee------------..eee...hhhhhhh.....ee......eeeeeeeeee......----........eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh.....eeeeeeeee....eeeeeeeeee..hhhhhhhh.ee...---.......eeeeeeeeehhhhhhhhhhhhh...eee.hhhhhh........eee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------N---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vbb A   2 VLDLDLFRVDKGGDPALIRETQEKRFKDPGLVDQLVKADSEWRRCRFRADNLNKLKNLCSKTIGEKMKKKE----DESVPENVLSFDDLTADALANLKVSQIKKVRLLIDEAILKCDAERIKLEAERFENLREIGNLLHPSVPISNDEDVDNKVERIWGDCTVRKKYSHVDLVVMVDGFEGEKGAVVAGSRGYFLKGVLVFLEQALIQYALRTLGSRGYIPIYTPFFMRKEVMQEVAQLS-FDEELYKVI------------DEKYLIATSEQPIAALHRDEWLRPEDLPIKYAGLSTCFRQEVGS----TRGIFRVHQFEKIEQFVYSSPHDNKSWEMFEEMITTAEEFYQSLGIPYHIVNIVSGSLNHAASKKLDLEAWFPGSGAFRELVSCSNCTDYQARRLRIRYGQT---MDKVEFVHMLNATMCATTRTICAILENYQTEKGITVPEKLKEFMPPGLQELIPFVKPAPI 476
                                    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         -  |    271       281       291       301     |   -|      321       331       341       351       361       371       381       391       401       411 |   | 421       431       441       451       461       471     
                                                                                                 72   77                                                                                                                                                                 241 |     251          264                                        307  312                                                                                                  413 417                                                           
                                                                                                                                                                                                                                                                           243                                                                                                                                                                                                                                         

Chain B from PDB  Type:PROTEIN  Length:454
 aligned with SYSC_HUMAN | P49591 from UniProtKB/Swiss-Prot  Length:514

    Alignment length:474
                                    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       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471    
           SYSC_HUMAN     2 VLDLDLFRVDKGGDPALIRETQEKRFKDPGLVDQLVKADSEWRRCRFRADNLNKLKNLCSKTIGEKMKKKEPVGDDESVPENVLSFDDLTADALANLKVSQIKKVRLLIDEAILKCDAERIKLEAERFENLREIGNLLHPSVPISNDEDVDNKVERIWGDCTVRKKYSHVDLVVMVDGFEGEKGAVVAGSRGYFLKGVLVFLEQALIQYALRTLGSRGYIPIYTPFFMRKEVMQEVAQLSQFDEELYKVIGKGSEKSDDNSYDEKYLIATSEQPIAALHRDEWLRPEDLPIKYAGLSTCFRQEVGSHGRDTRGIFRVHQFEKIEQFVYSSPHDNKSWEMFEEMITTAEEFYQSLGIPYHIVNIVSGSLNHAASKKLDLEAWFPGSGAFRELVSCSNCTDYQARRLRIRYGQTKKMMDKVEFVHMLNATMCATTRTICAILENYQTEKGITVPEKLKEFMPPGLQELIPFVKPAP 475
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..------..............hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhheeeeee.........hhhhhhhhh..eehhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhh..eeee...eeehhhhhhhh..hhhhhh.eee.------------..eee...hhhhhhh....eeehhhhh.eeeeeeeeee........--........eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh.....eeeeeeeee....eeeeeeeeee..hhhhhhh.eee.............eeeeeeeeehhhhhhhhhhhhh...eee.hhhhhhhh......eee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------N--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vbb B   2 VLDLDLFRVDKGGDPALIRETQEKRFKDPGLVDQLVKADSEWRRCRFRADNLNKLKNLCSKTIGEKMKK------DESVPENVLSFDDLTADALANLKVSQIKKVRLLIDEAILKCDAERIKLEAERFENLREIGNLLHPSVPISNDEDVDNKVERIWGDCTVRKKYSHVDLVVMVDGFEGEKGAVVAGSRGYFLKGVLVFLEQALIQYALRTLGSRGYIPIYTPFFMRKEVMQEVAQLSQFDEELYKVI------------DEKYLIATSEQPIAALHRDEWLRPEDLPIKYAGLSTCFRQEVGSHG--TRGIFRVHQFEKIEQFVYSSPHDNKSWEMFEEMITTAEEFYQSLGIPYHIVNIVSGSLNHAASKKLDLEAWFPGSGAFRELVSCSNCTDYQARRLRIRYGQTKKMMDKVEFVHMLNATMCATTRTICAILENYQTEKGITVPEKLKEFMPPGLQELIPFVKPAP 475
                                    11        21        31        41        51        61        |-     |  81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251         -  |    271       281       291       301       | -|      321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471    
                                                                                               70     77                                                                                                                                                                           251          264                                          309  |                                                                                                                                                                   
                                                                                                                                                                                                                                                                                                                                                312                                                                                                                                                                   

Chain C from PDB  Type:PROTEIN  Length:456
 aligned with SYSC_HUMAN | P49591 from UniProtKB/Swiss-Prot  Length:514

    Alignment length:474
                                    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       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471    
           SYSC_HUMAN     2 VLDLDLFRVDKGGDPALIRETQEKRFKDPGLVDQLVKADSEWRRCRFRADNLNKLKNLCSKTIGEKMKKKEPVGDDESVPENVLSFDDLTADALANLKVSQIKKVRLLIDEAILKCDAERIKLEAERFENLREIGNLLHPSVPISNDEDVDNKVERIWGDCTVRKKYSHVDLVVMVDGFEGEKGAVVAGSRGYFLKGVLVFLEQALIQYALRTLGSRGYIPIYTPFFMRKEVMQEVAQLSQFDEELYKVIGKGSEKSDDNSYDEKYLIATSEQPIAALHRDEWLRPEDLPIKYAGLSTCFRQEVGSHGRDTRGIFRVHQFEKIEQFVYSSPHDNKSWEMFEEMITTAEEFYQSLGIPYHIVNIVSGSLNHAASKKLDLEAWFPGSGAFRELVSCSNCTDYQARRLRIRYGQTKKMMDKVEFVHMLNATMCATTRTICAILENYQTEKGITVPEKLKEFMPPGLQELIPFVKPAP 475
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...---....hhhhh......hhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..................eeeeee.........hhhhhhhhh..eehhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhh...eeee...eeehhhhhhhh..........ee...---------...eee...hhhhhhhhhh..ee......eeeeeeeeee...------.........eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh.....eeeeeeeee....eeeeeeeeee.hhhhhhhh..ee.............eeeeeeeeehhhhhhhhhhhhh...ee..hhhhhh.........ee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------N--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vbb C   2 VLDLDLFRVDKGGDPALIRETQEKRFKDPGLVDQLVKADSEWRRCRFRADNLNKLKNLCSKTIGEKMKKKEP---DESVPENVLSFDDLTADALANLKVSQIKKVRLLIDEAILKCDAERIKLEAERFENLREIGNLLHPSVPISNDEDVDNKVERIWGDCTVRKKYSHVDLVVMVDGFEGEKGAVVAGSRGYFLKGVLVFLEQALIQYALRTLGSRGYIPIYTPFFMRKEVMQEVAQLSQFDEELYKVIGK---------YDEKYLIATSEQPIAALHRDEWLRPEDLPIKYAGLSTCFRQE------DTRGIFRVHQFEKIEQFVYSSPHDNKSWEMFEEMITTAEEFYQSLGIPYHIVNIVSGSLNHAASKKLDLEAWFPGSGAFRELVSCSNCTDYQARRLRIRYGQTKKMMDKVEFVHMLNATMCATTRTICAILENYQTEKGITVPEKLKEFMPPGLQELIPFVKPAP 475
                                    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 |       - |     271       281       291       301  |    311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471    
                                                                                                  73  77                                                                                                                                                                             253       263                                      304    311                                                                                                                                                                    

Chain D from PDB  Type:PROTEIN  Length:450
 aligned with SYSC_HUMAN | P49591 from UniProtKB/Swiss-Prot  Length:514

    Alignment length:475
                                    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       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471     
           SYSC_HUMAN     2 VLDLDLFRVDKGGDPALIRETQEKRFKDPGLVDQLVKADSEWRRCRFRADNLNKLKNLCSKTIGEKMKKKEPVGDDESVPENVLSFDDLTADALANLKVSQIKKVRLLIDEAILKCDAERIKLEAERFENLREIGNLLHPSVPISNDEDVDNKVERIWGDCTVRKKYSHVDLVVMVDGFEGEKGAVVAGSRGYFLKGVLVFLEQALIQYALRTLGSRGYIPIYTPFFMRKEVMQEVAQLSQFDEELYKVIGKGSEKSDDNSYDEKYLIATSEQPIAALHRDEWLRPEDLPIKYAGLSTCFRQEVGSHGRDTRGIFRVHQFEKIEQFVYSSPHDNKSWEMFEEMITTAEEFYQSLGIPYHIVNIVSGSLNHAASKKLDLEAWFPGSGAFRELVSCSNCTDYQARRLRIRYGQTKKMMDKVEFVHMLNATMCATTRTICAILENYQTEKGITVPEKLKEFMPPGLQELIPFVKPAPI 476
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....--....---.........hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhheeeeee.........hhhhhhhhh..eehhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhh..eeee...eeehhhhh......-......eee..----------..eee...hhhhhhhhhh..eehhhhh.eeeeeeeeee....------........eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh.....eeeeeeeee....eeeeeeeeee.hhhhhhhhh.ee..---........eeeeeeeeehhhhhhhhhhhhh...eee.hhhhhh........eee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------N---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vbb D   2 VLDLDLFRVDKGGDPALIRETQEKRFKDPGLVDQLVKADSEWRRCRFRADNLNKLKNLCSKTIGEKMKKKE--GDDE---ENVLSFDDLTADALANLKVSQIKKVRLLIDEAILKCDAERIKLEAERFENLREIGNLLHPSVPISNDEDVDNKVERIWGDCTVRKKYSHVDLVVMVDGFEGEKGAVVAGSRGYFLKGVLVFLEQALIQYALRTLGSRGYIPIYTPFFMRKEVMQEVAQLS-FDEELYKVIGK----------DEKYLIATSEQPIAALHRDEWLRPEDLPIKYAGLSTCFRQEV------TRGIFRVHQFEKIEQFVYSSPHDNKSWEMFEEMITTAEEFYQSLGIPYHIVNIVSGSLNHAASKKLDLEAWFPGSGAFRELVSCSNCTDYQARRLRIRYGQ---MMDKVEFVHMLNATMCATTRTICAILENYQTEKGITVPEKLKEFMPPGLQELIPFVKPAPI 476
                                    11        21        31        41        51        61        71|  |  |  -|       91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241 |     251 |       -  |    271       281       291       301   |     -|      321       331       341       351       361       371       381       391       401       411|   |  421       431       441       451       461       471     
                                                                                                 72 75 78  82                                                                                                                                                            241 |       253        264                                      305    312                                                                                                 412 416                                                            
                                                                                                                                                                                                                                                                           243                                                                                                                                                                                                                                         

Chain E from PDB  Type:PROTEIN  Length:440
 aligned with SYSC_HUMAN | P49591 from UniProtKB/Swiss-Prot  Length:514

    Alignment length:475
                                    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       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471     
           SYSC_HUMAN     2 VLDLDLFRVDKGGDPALIRETQEKRFKDPGLVDQLVKADSEWRRCRFRADNLNKLKNLCSKTIGEKMKKKEPVGDDESVPENVLSFDDLTADALANLKVSQIKKVRLLIDEAILKCDAERIKLEAERFENLREIGNLLHPSVPISNDEDVDNKVERIWGDCTVRKKYSHVDLVVMVDGFEGEKGAVVAGSRGYFLKGVLVFLEQALIQYALRTLGSRGYIPIYTPFFMRKEVMQEVAQLSQFDEELYKVIGKGSEKSDDNSYDEKYLIATSEQPIAALHRDEWLRPEDLPIKYAGLSTCFRQEVGSHGRDTRGIFRVHQFEKIEQFVYSSPHDNKSWEMFEEMITTAEEFYQSLGIPYHIVNIVSGSLNHAASKKLDLEAWFPGSGAFRELVSCSNCTDYQARRLRIRYGQTKKMMDKVEFVHMLNATMCATTRTICAILENYQTEKGITVPEKLKEFMPPGLQELIPFVKPAPI 476
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....----------------.......hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhheeeeee.........hhhhhhhhh..eehhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhh...eeee......hhhhhhhh..-----...eee..---------..eee....hhhhhhhhhh..ee......eeeeeeeeee......-----.......eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh.....eeeeeeeee....eeeeeeeeee..hhhhhhh..ee.............eeeeeeeeehhhhhhhhhhhh....eee.hhhhhh..hhhhh.eee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------N---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vbb E   2 VLDLDLFRVDKGGDPALIRETQEKRFKDPGLVDQLVKADSEWRRCRFRADNLNKLKNLCSKTIGEK----------------VLSFDDLTADALANLKVSQIKKVRLLIDEAILKCDAERIKLEAERFENLREIGNLLHPSVPISNDEDVDNKVERIWGDCTVRKKYSHVDLVVMVDGFEGEKGAVVAGSRGYFLKGVLVFLEQALIQYALRTLGSRGYIPIYTPFFMRKEVMQEVAQL-----ELYKVIGK---------YDEKYLIATSEQPIAALHRDEWLRPEDLPIKYAGLSTCFRQEVGS-----RGIFRVHQFEKIEQFVYSSPHDNKSWEMFEEMITTAEEFYQSLGIPYHIVNIVSGSLNHAASKKLDLEAWFPGSGAFRELVSCSNCTDYQARRLRIRYGQTKKMMDKVEFVHMLNATMCATTRTICAILENYQTEKGITVPEKLKEFMPPGLQELIPFVKPAPI 476
                                    11        21        31        41        51        61     |   -         -  |     91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        |-    |  251 |       - |     271       281       291       301     |   - |     321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471     
                                                                                            67               84                                                                                                                                                         240   246    253       263                                         307   313                                                                                                                                                                   

Chain F from PDB  Type:PROTEIN  Length:443
 aligned with SYSC_HUMAN | P49591 from UniProtKB/Swiss-Prot  Length:514

    Alignment length:475
                                    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       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471     
           SYSC_HUMAN     2 VLDLDLFRVDKGGDPALIRETQEKRFKDPGLVDQLVKADSEWRRCRFRADNLNKLKNLCSKTIGEKMKKKEPVGDDESVPENVLSFDDLTADALANLKVSQIKKVRLLIDEAILKCDAERIKLEAERFENLREIGNLLHPSVPISNDEDVDNKVERIWGDCTVRKKYSHVDLVVMVDGFEGEKGAVVAGSRGYFLKGVLVFLEQALIQYALRTLGSRGYIPIYTPFFMRKEVMQEVAQLSQFDEELYKVIGKGSEKSDDNSYDEKYLIATSEQPIAALHRDEWLRPEDLPIKYAGLSTCFRQEVGSHGRDTRGIFRVHQFEKIEQFVYSSPHDNKSWEMFEEMITTAEEFYQSLGIPYHIVNIVSGSLNHAASKKLDLEAWFPGSGAFRELVSCSNCTDYQARRLRIRYGQTKKMMDKVEFVHMLNATMCATTRTICAILENYQTEKGITVPEKLKEFMPPGLQELIPFVKPAPI 476
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....------...................-.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhheeeeee.........hhhhhhhhh..ee..hhhhhhh....eeehhhhhhhhhhhhhhhhhhhhh..eeee...eeehhhhhhh..-----...eee..---------....eee...hhhhhhhhhh..........eeeeeeeeee....------........eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh.....eeeeeeeee....eeeeeeeeee..hhhhhhh......-----......eeeeeeeeehhhhhhhhhhhhh...eee.hhhhhh........eee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------N---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vbb F   2 VLDLDLFRVDKGGDPALIRETQEKRFKDPGLVDQLVKADSEWRRCRFRADNLNKLKNLCSKTIGEKMKKKEP------VPENVLSFDDLTADALANL-VSQIKKVRLLIDEAILKCDAERIKLEAERFENLREIGNLLHPSVPISNDEDVDNKVERIWGDCTVRKKYSHVDLVVMVDGFEGEKGAVVAGSRGYFLKGVLVFLEQALIQYALRTLGSRGYIPIYTPFFMRKEVMQEVAQ-----EELYKVIG---------SYDEKYLIATSEQPIAALHRDEWLRPEDLPIKYAGLSTCFRQEV------TRGIFRVHQFEKIEQFVYSSPHDNKSWEMFEEMITTAEEFYQSLGIPYHIVNIVSGSLNHAASKKLDLEAWFPGSGAFRELVSCSNCTDYQARRLRIRYGQ-----DKVEFVHMLNATMCATTRTICAILENYQTEKGITVPEKLKEFMPPGLQELIPFVKPAPI 476
                                    11        21        31        41        51        61        71 |      81        91      |101       111       121       131       141       151       161       171       181       191       201       211       221       231       | -   |   251|        -|      271       281       291       301   |     -|      321       331       341       351       361       371       381       391       401       411|     |421       431       441       451       461       471     
                                                                                                  73     80                98 |                                                                                                                                        239   245    252       262                                        305    312                                                                                                 412   418                                                          
                                                                                                                            100                                                                                                                                                                                                                                                                                                                                                                                        

   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 3VBB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VBB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VBB)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (SYSC_HUMAN | P49591)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004812    aminoacyl-tRNA ligase activity    Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    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.
    GO:0098619    selenocysteine-tRNA ligase activity    Catalysis of the reaction: tRNASec + L-Ser + ATP ---> Ser-tRNASec + AMP + Diphosphate.
    GO:0004828    serine-tRNA ligase activity    Catalysis of the reaction: ATP + L-serine + tRNA(Ser) = AMP + diphosphate + L-seryl-tRNA(Ser).
biological process
    GO:0016259    selenocysteine metabolic process    The chemical reactions and pathways involving selenocysteine, an essential component of glutathione peroxidase and some other proteins.
    GO:0097056    selenocysteinyl-tRNA(Sec) biosynthetic process    The chemical reactions and pathways resulting in the formation of selenocysteinyl-tRNA(Sec). This process occurs through the following steps: a unique serine-tRNA with a UGA recognizing anticodon is first aminoacylated with serine; this is then phosphorylated by phosphoseryl-tRNA[Ser]Sec kinase; lastly, selenium is swapped for the phosphate on the serine.
    GO:0006434    seryl-tRNA aminoacylation    The process of coupling serine to seryl-tRNA, catalyzed by seryl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA.
    GO:0006418    tRNA aminoacylation for protein translation    The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, to be used in ribosome-mediated polypeptide synthesis.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SYSC_HUMAN | P495914l87 4rqe 4rqf

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3VBB)