Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
(-)Biological Unit 5
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)
Image Biological Unit 5
Biological Unit 5  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF ARCHAEAL O-PHOSPHOSERYL-TRNA(SEC) SELENIUM TRANSFERASE (SEPSECS)
 
Authors :  Y. Araiso, R. Ishitani, S. Pailouer, H. Oshikane, N. Domae, D. Soll, O. N
Date :  23 Jul 07  (Deposition) - 29 Apr 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A,B  (1x)
Biol. Unit 4:  A,D  (1x)
Biol. Unit 5:  B,C  (1x)
Keywords :  Selenocysteine Biosynthesis, Seven-Stranded Bete-Strand, Pyridoxal- 5'-Phosphate, Protein Biosynthesis, Pyridoxal Phosphate, Selenium, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Araiso, S. Palioura, R. Ishitani, R. L. Sherrer, P. O'Donoghue, J. Yuan, H. Oshikane, N. Domae, J. Defranco, D. Soll, O. Nureki
Structural Insights Into Rna-Dependent Eukaryal And Archaea Selenocysteine Formation.
Nucleic Acids Res. V. 36 1187 2008
PubMed-ID: 18158303  |  Reference-DOI: 10.1093/NAR/GKM1122

(-) Compounds

Molecule 1 - O-PHOSPHOSERYL-TRNA(SEC) SELENIUM TRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.9.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: B834(DE3)CODON PLUS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SPCS
    Organism Scientific: METHANOCOCCUS MARIPALUDIS
    Organism Taxid: 267377
    Strain: S2
    Synonym: SELENOCYSTEINE SYNTHASE, SEC SYNTHASE, SELENOCYSTEINYL-
    Trnasec, Synthase, Sep-trna: SEC-TRNA SYNTHASE, SEPSECS

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD
Biological Unit 2 (1x):   CD
Biological Unit 3 (1x): AB  
Biological Unit 4 (1x): A  D
Biological Unit 5 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 46)

Asymmetric Unit (3, 46)
No.NameCountTypeFull Name
1MSE40Mod. Amino AcidSELENOMETHIONINE
2PLP4Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 46)
No.NameCountTypeFull Name
1MSE40Mod. Amino AcidSELENOMETHIONINE
2PLP4Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3SO42Ligand/IonSULFATE ION
Biological Unit 2 (3, 23)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3SO41Ligand/IonSULFATE ION
Biological Unit 3 (3, 23)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3SO41Ligand/IonSULFATE ION
Biological Unit 4 (2, 22)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3SO4-1Ligand/IonSULFATE ION
Biological Unit 5 (3, 24)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:94 , SER B:95 , GLN B:102 , ARG B:307 , HOH B:1005BINDING SITE FOR RESIDUE SO4 B 1002
2AC2SOFTWAREARG C:94 , SER C:95 , GLN C:102 , ARG C:307BINDING SITE FOR RESIDUE SO4 C 1002
3AC3SOFTWARESER A:138 , THR A:139 , GLY A:140 , HIS A:166 , SER A:168 , THR A:220 , ASN A:247 , ALA A:249 , TYR A:250 , LYS A:278 , GLU B:71 , ARG B:72 , GLY B:306 , ARG B:307BINDING SITE FOR RESIDUE PLP A 1001
4AC4SOFTWAREARG A:72 , GLY A:306 , ARG A:307 , SER B:138 , THR B:139 , GLY B:140 , HIS B:166 , SER B:168 , THR B:220 , PHE B:221 , ASN B:247 , ALA B:249 , LYS B:278 , HOH B:1029BINDING SITE FOR RESIDUE PLP B 1001
5AC5SOFTWARESER C:138 , THR C:139 , GLY C:140 , HIS C:166 , SER C:168 , THR C:220 , PHE C:221 , ASN C:247 , TYR C:250 , LYS C:278 , ARG D:72 , GLY D:306 , ARG D:307BINDING SITE FOR RESIDUE PLP C 1001
6AC6SOFTWAREARG C:72 , GLY C:306 , ARG C:307 , SER D:138 , THR D:139 , GLY D:140 , HIS D:166 , SER D:168 , THR D:220 , PHE D:221 , ASN D:247 , ALA D:249 , LYS D:278BINDING SITE FOR RESIDUE PLP D 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z67)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Z67)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z67)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z67)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z67)

(-) 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:434
 aligned with SPCS_METMP | Q6LZM9 from UniProtKB/Swiss-Prot  Length:436

    Alignment length:434
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430    
           SPCS_METMP     1 MLDFNIEGLIPKNMEKRGELVLNEYLKEIEDVFNHRKIPENGIDDEKIKLFLKFLSMMDTDKDPKSVRIGEREARTYSKIHEELSSGFCHGIGRSGNLVDPQPKASGASIMYALTNKILESFFKQLGLNVHAIATPISTGMSISLCLSAARKKYGSNVVIYPYASHKSPIKAVSFVGMNMRLVETVLDGDRVYVPVEDIENAIKKEIELGNRPCVLSTLTFFPPRNSDDIVEIAKICENYDIPHIINGAYAIQNNYYLEKLKKAFKYRVDAVVSSSDKNLLTPIGGGLVYSTDAEFIKEISLSYPGRASATPVVNTLVSLLSMGSKNYLELVKNQKNSKKLLDELLNDLSKKTGGKFLDVESPIASCISVNSDPVEIAAKLYNLRVTGPRGIKKTDHFGNCYLGTYTHDYIVMNAAIGVRTEDIVNSVSKLEKI 434
               SCOP domains d2z67a1 A:1-434 Selenocysteinyl-tRNA synthase (SepSecS)                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh...ee.........hhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhh..eeeee..eee..eee.hhhhhhhhhhhhhhh...eeeeee..........hhhhhhhhhhhhh..eeee......hhhhhhhhhhhhh....eeeeehhhhhh.....eeeee.hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeeee...hhhhhhhhhhhh.ee..eee...hhhhhh........eeeee.....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z67 A   1 mLDFNIEGLIPKNmEKRGELVLNEYLKEIEDVFNHRKIPENGIDDEKIKLFLKFLSmmDTDKDPKSVRIGEREARTYSKIHEELSSGFCHGIGRSGNLVDPQPKASGASImYALTNKILESFFKQLGLNVHAIATPISTGmSISLCLSAARKKYGSNVVIYPYASHKSPIKAVSFVGmNmRLVETVLDGDRVYVPVEDIENAIKKEIELGNRPCVLSTLTFFPPRNSDDIVEIAKICENYDIPHIINGAYAIQNNYYLEKLKKAFKYRVDAVVSSSDKNLLTPIGGGLVYSTDAEFIKEISLSYPGRASATPVVNTLVSLLSmGSKNYLELVKNQKNSKKLLDELLNDLSKKTGGKFLDVESPIASCISVNSDPVEIAAKLYNLRVTGPRGIKKTDHFGNCYLGTYTHDYIVmNAAIGVRTEDIVNSVSKLEKI 434
                            |       10   |    20        30        40        50      ||60        70        80        90       100       110|      120       130       140|      150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320  |    330       340       350       360       370       380       390       400       410  |    420       430    
                            |           14-MSE                                     57-MSE                                               111-MSE                       141-MSE                              178-MSE                                                                                                                                          323-MSE                                                                                   413-MSE                 
                            1-MSE                                                   58-MSE                                                                                                                   180-MSE                                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:434
 aligned with SPCS_METMP | Q6LZM9 from UniProtKB/Swiss-Prot  Length:436

    Alignment length:434
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430    
           SPCS_METMP     1 MLDFNIEGLIPKNMEKRGELVLNEYLKEIEDVFNHRKIPENGIDDEKIKLFLKFLSMMDTDKDPKSVRIGEREARTYSKIHEELSSGFCHGIGRSGNLVDPQPKASGASIMYALTNKILESFFKQLGLNVHAIATPISTGMSISLCLSAARKKYGSNVVIYPYASHKSPIKAVSFVGMNMRLVETVLDGDRVYVPVEDIENAIKKEIELGNRPCVLSTLTFFPPRNSDDIVEIAKICENYDIPHIINGAYAIQNNYYLEKLKKAFKYRVDAVVSSSDKNLLTPIGGGLVYSTDAEFIKEISLSYPGRASATPVVNTLVSLLSMGSKNYLELVKNQKNSKKLLDELLNDLSKKTGGKFLDVESPIASCISVNSDPVEIAAKLYNLRVTGPRGIKKTDHFGNCYLGTYTHDYIVMNAAIGVRTEDIVNSVSKLEKI 434
               SCOP domains d2z67b_ B: Selenocysteinyl-tRNA synthase (SepSecS)                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh...ee.........hhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhh..eeeee..eee..eee.hhhhhhhhhhhhhhh...eeeeee..........hhhhhhhhhhhh...eeee......hhhhhhhhhhhh.....eeeeehhhhhh.....eeeee.hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeee...hhhhhhhhhhhh.ee..eee.................eeeee.....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z67 B   1 mLDFNIEGLIPKNmEKRGELVLNEYLKEIEDVFNHRKIPENGIDDEKIKLFLKFLSmmDTDKDPKSVRIGEREARTYSKIHEELSSGFCHGIGRSGNLVDPQPKASGASImYALTNKILESFFKQLGLNVHAIATPISTGmSISLCLSAARKKYGSNVVIYPYASHKSPIKAVSFVGmNmRLVETVLDGDRVYVPVEDIENAIKKEIELGNRPCVLSTLTFFPPRNSDDIVEIAKICENYDIPHIINGAYAIQNNYYLEKLKKAFKYRVDAVVSSSDKNLLTPIGGGLVYSTDAEFIKEISLSYPGRASATPVVNTLVSLLSmGSKNYLELVKNQKNSKKLLDELLNDLSKKTGGKFLDVESPIASCISVNSDPVEIAAKLYNLRVTGPRGIKKTDHFGNCYLGTYTHDYIVmNAAIGVRTEDIVNSVSKLEKI 434
                            |       10   |    20        30        40        50      ||60        70        80        90       100       110|      120       130       140|      150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320  |    330       340       350       360       370       380       390       400       410  |    420       430    
                            1-MSE       14-MSE                                     57-MSE                                               111-MSE                       141-MSE                              178-MSE                                                                                                                                          323-MSE                                                                                   413-MSE                 
                                                                                    58-MSE                                                                                                                   180-MSE                                                                                                                                                                                                                                                          


Chain C from PDB  Type:PROTEIN  Length:434
 aligned with SPCS_METMP | Q6LZM9 from UniProtKB/Swiss-Prot  Length:436

    Alignment length:434
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430    
           SPCS_METMP     1 MLDFNIEGLIPKNMEKRGELVLNEYLKEIEDVFNHRKIPENGIDDEKIKLFLKFLSMMDTDKDPKSVRIGEREARTYSKIHEELSSGFCHGIGRSGNLVDPQPKASGASIMYALTNKILESFFKQLGLNVHAIATPISTGMSISLCLSAARKKYGSNVVIYPYASHKSPIKAVSFVGMNMRLVETVLDGDRVYVPVEDIENAIKKEIELGNRPCVLSTLTFFPPRNSDDIVEIAKICENYDIPHIINGAYAIQNNYYLEKLKKAFKYRVDAVVSSSDKNLLTPIGGGLVYSTDAEFIKEISLSYPGRASATPVVNTLVSLLSMGSKNYLELVKNQKNSKKLLDELLNDLSKKTGGKFLDVESPIASCISVNSDPVEIAAKLYNLRVTGPRGIKKTDHFGNCYLGTYTHDYIVMNAAIGVRTEDIVNSVSKLEKI 434
               SCOP domains d2z67c_ C: Selenocysteinyl-tRNA synthase (SepSecS)                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh...ee.........hhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhh..eeeee..eee..eee.hhhhhhhhhhhhhhh...eeeeee..........hhhhhhhhhhhhh..eeee......hhhhhhhhhhhh.....eeeeehhhhhh.....eeeee.hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeeee...hhhhhhhhhhh..ee..eee...hhhhhh........eeeee.....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z67 C   1 mLDFNIEGLIPKNmEKRGELVLNEYLKEIEDVFNHRKIPENGIDDEKIKLFLKFLSmmDTDKDPKSVRIGEREARTYSKIHEELSSGFCHGIGRSGNLVDPQPKASGASImYALTNKILESFFKQLGLNVHAIATPISTGmSISLCLSAARKKYGSNVVIYPYASHKSPIKAVSFVGmNmRLVETVLDGDRVYVPVEDIENAIKKEIELGNRPCVLSTLTFFPPRNSDDIVEIAKICENYDIPHIINGAYAIQNNYYLEKLKKAFKYRVDAVVSSSDKNLLTPIGGGLVYSTDAEFIKEISLSYPGRASATPVVNTLVSLLSmGSKNYLELVKNQKNSKKLLDELLNDLSKKTGGKFLDVESPIASCISVNSDPVEIAAKLYNLRVTGPRGIKKTDHFGNCYLGTYTHDYIVmNAAIGVRTEDIVNSVSKLEKI 434
                            |       10   |    20        30        40        50      ||60        70        80        90       100       110|      120       130       140|      150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320  |    330       340       350       360       370       380       390       400       410  |    420       430    
                            1-MSE       14-MSE                                     57-MSE                                               111-MSE                       141-MSE                              178-MSE                                                                                                                                          323-MSE                                                                                   413-MSE                 
                                                                                    58-MSE                                                                                                                   180-MSE                                                                                                                                                                                                                                                          


Chain D from PDB  Type:PROTEIN  Length:434
 aligned with SPCS_METMP | Q6LZM9 from UniProtKB/Swiss-Prot  Length:436

    Alignment length:434
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430    
           SPCS_METMP     1 MLDFNIEGLIPKNMEKRGELVLNEYLKEIEDVFNHRKIPENGIDDEKIKLFLKFLSMMDTDKDPKSVRIGEREARTYSKIHEELSSGFCHGIGRSGNLVDPQPKASGASIMYALTNKILESFFKQLGLNVHAIATPISTGMSISLCLSAARKKYGSNVVIYPYASHKSPIKAVSFVGMNMRLVETVLDGDRVYVPVEDIENAIKKEIELGNRPCVLSTLTFFPPRNSDDIVEIAKICENYDIPHIINGAYAIQNNYYLEKLKKAFKYRVDAVVSSSDKNLLTPIGGGLVYSTDAEFIKEISLSYPGRASATPVVNTLVSLLSMGSKNYLELVKNQKNSKKLLDELLNDLSKKTGGKFLDVESPIASCISVNSDPVEIAAKLYNLRVTGPRGIKKTDHFGNCYLGTYTHDYIVMNAAIGVRTEDIVNSVSKLEKI 434
               SCOP domains d2z67d_ D: Selenocysteinyl-tRNA synthase (SepSecS)                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------SLA_LP_auto_ag-2z67D01 D:58-434                                                                                                                                                                                                                                                                                                                                                           Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------SLA_LP_auto_ag-2z67D02 D:58-434                                                                                                                                                                                                                                                                                                                                                           Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------SLA_LP_auto_ag-2z67D03 D:58-434                                                                                                                                                                                                                                                                                                                                                           Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------SLA_LP_auto_ag-2z67D04 D:58-434                                                                                                                                                                                                                                                                                                                                                           Pfam domains (4)
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh...ee.........hhhhhhhh....................hhhhhhhhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhh..eeeee..eee..eee.hhhhhhhhhhhhhhh...eeeeee..........hhhhhhhhhhhhh..eeee......hhhhhhhhhhhh.....eeeeehhhhh......eeeee.hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeeee...hhhhhhhhhhh..ee..eee...hhhhhh........eeeee.....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z67 D   1 mLDFNIEGLIPKNmEKRGELVLNEYLKEIEDVFNHRKIPENGIDDEKIKLFLKFLSmmDTDKDPKSVRIGEREARTYSKIHEELSSGFCHGIGRSGNLVDPQPKASGASImYALTNKILESFFKQLGLNVHAIATPISTGmSISLCLSAARKKYGSNVVIYPYASHKSPIKAVSFVGmNmRLVETVLDGDRVYVPVEDIENAIKKEIELGNRPCVLSTLTFFPPRNSDDIVEIAKICENYDIPHIINGAYAIQNNYYLEKLKKAFKYRVDAVVSSSDKNLLTPIGGGLVYSTDAEFIKEISLSYPGRASATPVVNTLVSLLSmGSKNYLELVKNQKNSKKLLDELLNDLSKKTGGKFLDVESPIASCISVNSDPVEIAAKLYNLRVTGPRGIKKTDHFGNCYLGTYTHDYIVmNAAIGVRTEDIVNSVSKLEKI 434
                            |       10   |    20        30        40        50      ||60        70        80        90       100       110|      120       130       140|      150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320  |    330       340       350       360       370       380       390       400       410  |    420       430    
                            1-MSE       14-MSE                                     57-MSE                                               111-MSE                       141-MSE                              178-MSE                                                                                                                                          323-MSE                                                                                   413-MSE                 
                                                                                    58-MSE                                                                                                                   180-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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Z67)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: PLP_aminotran (240)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (SPCS_METMP | Q6LZM9)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016785    transferase activity, transferring selenium-containing groups    Catalysis of the transfer of a selenium-containing group from one compound (donor) to another (acceptor).
biological process
    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: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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PLP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2z67)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]
    Biological Unit 5  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 PNG format | Biol. Unit 5 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2z67
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SPCS_METMP | Q6LZM9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.9.1.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  SPCS_METMP | Q6LZM9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2Z67)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2Z67)