3KT8 - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF S. CEREVISIAE TRYPTOPHANYL-TRNA SYNTHETASE IN COMPLEX WITH L-TRYPTOPHANAMIDE

Authors :   M. Zhou, X. Dong, C. Zhong, N. Shen, J. Ding

Date :   24 Nov 09 (Deposition) - 16 Feb 10 (Release) - 16 Jun 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Tryptophanyl-Trna Synthetase, S. Cerevisiae, Sulfate Ion, Amino Acid Activation, Catalytic Mechanism, Tryptophanamide, Aminoacyl-Trna Synthetase, Atp-Binding, Cytoplasm, Ligase, Nucleotide-Binding, Protein Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Zhou, X. Dong, N. Shen, C. Zhong, J. Ding
Crystal Structures Of Saccharomyces Cerevisiae Tryptophanyl-Trna Synthetase: New Insights Into The Mechanism Of Tryptophan Activation And Implications For Anti-Fungal Drug Design
Nucleic Acids Res. V. 38 3399 2010
PubMed-ID: 20123733 | Reference-DOI: 10.1093/NAR/GKP1254

Molecule 1 - TRYPTOPHANYL-TRNA SYNTHETASE, CYTOPLASMIC
	Chains	:	A, B, C, D
	EC Number	:	6.1.1.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET3E
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	TRPS
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	TRYPTOPHAN--TRNA LIGASE, TRPRS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 14)

No.	Name	Count	Type	Full Name
1	LTN	4	Ligand/Ion	L-TRYPTOPHANAMIDE
2	SO4	10	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	LTN	2	Ligand/Ion	L-TRYPTOPHANAMIDE
2	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	LTN	2	Ligand/Ion	L-TRYPTOPHANAMIDE
2	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR A:106 , GLY A:108 , ARG A:109 , GLY A:110 , GLU A:141 , THR A:143 , GLU A:146 , LYS A:147 , GLN A:230 , CYS A:255 , GLN A:259 , PHE A:263 , SO4 A:441	BINDING SITE FOR RESIDUE LTN A 500
02	AC2	SOFTWARE	ARG A:73 , GLU A:74	BINDING SITE FOR RESIDUE SO4 A 439
03	AC3	SOFTWARE	PHE A:148 , THR A:155 , ILE A:156 , ARG B:199	BINDING SITE FOR RESIDUE SO4 A 440
04	AC4	SOFTWARE	HIS A:120 , LTN A:500	BINDING SITE FOR RESIDUE SO4 A 441
05	AC5	SOFTWARE	TYR B:106 , GLY B:108 , GLY B:110 , GLU B:141 , THR B:143 , GLU B:146 , LYS B:147 , GLN B:230 , CYS B:255 , GLN B:259 , PHE B:263	BINDING SITE FOR RESIDUE LTN B 700
06	AC6	SOFTWARE	ARG B:73 , GLU B:74	BINDING SITE FOR RESIDUE SO4 B 439
07	AC7	SOFTWARE	ARG A:199 , PHE B:148 , THR B:155 , ILE B:156	BINDING SITE FOR RESIDUE SO4 B 440
08	AC8	SOFTWARE	ARG B:109 , SER B:112 , HIS B:120 , SER B:297 , ALA B:298	BINDING SITE FOR RESIDUE SO4 B 441
09	AC9	SOFTWARE	TYR C:106 , GLY C:108 , ARG C:109 , GLY C:110 , GLU C:141 , THR C:143 , GLU C:146 , LYS C:147 , GLN C:230 , CYS C:255 , GLN C:259 , PHE C:263	BINDING SITE FOR RESIDUE LTN C 600
10	BC1	SOFTWARE	ARG C:73 , GLU C:74	BINDING SITE FOR RESIDUE SO4 C 439
11	BC2	SOFTWARE	ARG C:109 , SER C:112 , HIS C:117 , HIS C:120 , SER C:297 , ALA C:298 , HOH C:441	BINDING SITE FOR RESIDUE SO4 C 440
12	BC3	SOFTWARE	TYR D:106 , GLY D:108 , ARG D:109 , GLY D:110 , GLU D:141 , THR D:143 , GLU D:146 , LYS D:147 , GLN D:230 , CYS D:255 , GLN D:259 , PHE D:263 , SO4 D:439	BINDING SITE FOR RESIDUE LTN D 800
13	BC4	SOFTWARE	HIS D:120 , LTN D:800	BINDING SITE FOR RESIDUE SO4 D 439
14	BC5	SOFTWARE	ARG C:199 , PHE D:148 , THR D:155 , ILE D:156	BINDING SITE FOR RESIDUE SO4 D 440

(no "SS Bond" information available for 3KT8)

(no "Cis Peptide Bond" information available for 3KT8)

(no "SAP(SNP)/Variant" information available for 3KT8)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRNA_LIGASE_I	PS00178	Aminoacyl-transfer RNA synthetases class-I signature.	SYWC_YEAST	111-121	4	A:111-121 B:111-121 C:111-121 D:111-121

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRNA_LIGASE_I	PS00178	Aminoacyl-transfer RNA synthetases class-I signature.	SYWC_YEAST	111-121	2	A:111-121 B:111-121 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRNA_LIGASE_I	PS00178	Aminoacyl-transfer RNA synthetases class-I signature.	SYWC_YEAST	111-121	2	- - C:111-121 D:111-121

Asymmetric Unit (1, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YOL097C	1	YOL097C.1	XV:137825-136527	1299	SYWC_YEAST	1-432	432	4	A:18-425 B:23-425 C:23-425 D:16-425	408 403 403 410

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:408
 aligned with SYWC_YEAST | Q12109 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:408
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417        
           SYWC_YEAST    18 KSTDVKEQVVTPWDVEGGVDEQGRAQNIDYDKLIKQFGTKPVNEETLKRFKQVTGREPHHFLRKGLFFSERDFTKILDLYEQGKPFFLYTGRGPSSDSMHLGHMIPFVFTKWLQEVFDVPLVIELTDDEKFLFKHKLTINDVKNFARENAKDIIAVGFDPKNTFIFSDLQYMGGAFYETVVRVSRQITGSTAKAVFGFNDSDCIGKFHFASIQIATAFPSSFPNVLGLPDKTPCLIPCAIDQDPYFRVCRDVADKLKYSKPALLHSRFFPALQGSTTKMSASDDTTAIFMTDTPKQIQKKINKYAFSGGQVSADLHRELGGNPDVDVAYQYLSFFKDDDVFLKECYDKYKSGELLSGEMKKLCIETLQEFVKAFQERRAQVDEETLDKFMVPHKLVWGEKERLVAPKP 425
               SCOP domains d3kt8a_ A: Tryptophanyl-tRNA synthetase (TrpRS)                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........ee....ee..ee..ee....hhhhhhhhhh.ee.hhhhhhhhhhhhh...hhhhhh..eeeeehhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhh...hhhhhhhhhhhhhhhhhh.......eeeeehhhhhhhhhhhhhhhhhh..hhhhhhhhh......hhhhhhhhhhhhhhhhhhhh...........eeeeee..hhhhhhhhhhhhhhh.....eeeee..........................hhhhhhhhhhhh.......hhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------AA_TRNA_LIG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:18-425 UniProt: 1-432 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                      Transcript 1
                 3kt8 A  18 KSTDVKEQVVTPWDVEGGVDEQGRAQNIDYDKLIKQFGTKPVNEETLKRFKQVTGREPHHFLRKGLFFSERDFTKILDLYEQGKPFFLYTGRGPSSDSMHLGHMIPFVFTKWLQEVFDVPLVIELTDDEKFLFKHKLTINDVKNFARENAKDIIAVGFDPKNTFIFSDLQYMGGAFYETVVRVSRQITGSTAKAVFGFNDSDCIGKFHFASIQIATAFPSSFPNVLGLPDKTPCLIPCAIDQDPYFRVCRDVADKLKYSKPALLHSRFFPALQGSTTKMSASDDTTAIFMTDTPKQIQKKINKYAFSGGQVSADLHRELGGNPDVDVAYQYLSFFKDDDVFLKECYDKYKSGELLSGEMKKLCIETLQEFVKAFQERRAQVDEETLDKFMVPHKLVWGEKERLVAPKP 425
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417

Chain B from PDB  Type:PROTEIN  Length:403
 aligned with SYWC_YEAST | Q12109 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:403
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422   
           SYWC_YEAST    23 KEQVVTPWDVEGGVDEQGRAQNIDYDKLIKQFGTKPVNEETLKRFKQVTGREPHHFLRKGLFFSERDFTKILDLYEQGKPFFLYTGRGPSSDSMHLGHMIPFVFTKWLQEVFDVPLVIELTDDEKFLFKHKLTINDVKNFARENAKDIIAVGFDPKNTFIFSDLQYMGGAFYETVVRVSRQITGSTAKAVFGFNDSDCIGKFHFASIQIATAFPSSFPNVLGLPDKTPCLIPCAIDQDPYFRVCRDVADKLKYSKPALLHSRFFPALQGSTTKMSASDDTTAIFMTDTPKQIQKKINKYAFSGGQVSADLHRELGGNPDVDVAYQYLSFFKDDDVFLKECYDKYKSGELLSGEMKKLCIETLQEFVKAFQERRAQVDEETLDKFMVPHKLVWGEKERLVAPKP 425
               SCOP domains d3kt8b_ B: Tryptophanyl-tRNA synthetase (TrpRS)                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....ee............hhhhhhhhhh.ee.hhhhhhhhhhhhh...hhhhhh..eeeeehhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhh...hhhhhhhhhhhhhhhhhh.......eeeeehhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...........eeeeee..hhhhhhhhhhhhhhh.....eeeee..........................hhhhhhhhhhhhh......hhhhhhhhh.....hhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------AA_TRNA_LIG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:23-425 UniProt: 1-432 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                 Transcript 1
                 3kt8 B  23 KEQVVTPWDVEGGVDEQGRAQNIDYDKLIKQFGTKPVNEETLKRFKQVTGREPHHFLRKGLFFSERDFTKILDLYEQGKPFFLYTGRGPSSDSMHLGHMIPFVFTKWLQEVFDVPLVIELTDDEKFLFKHKLTINDVKNFARENAKDIIAVGFDPKNTFIFSDLQYMGGAFYETVVRVSRQITGSTAKAVFGFNDSDCIGKFHFASIQIATAFPSSFPNVLGLPDKTPCLIPCAIDQDPYFRVCRDVADKLKYSKPALLHSRFFPALQGSTTKMSASDDTTAIFMTDTPKQIQKKINKYAFSGGQVSADLHRELGGNPDVDVAYQYLSFFKDDDVFLKECYDKYKSGELLSGEMKKLCIETLQEFVKAFQERRAQVDEETLDKFMVPHKLVWGEKERLVAPKP 425
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422

Chain C from PDB  Type:PROTEIN  Length:403
 aligned with SYWC_YEAST | Q12109 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:403
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422   
           SYWC_YEAST    23 KEQVVTPWDVEGGVDEQGRAQNIDYDKLIKQFGTKPVNEETLKRFKQVTGREPHHFLRKGLFFSERDFTKILDLYEQGKPFFLYTGRGPSSDSMHLGHMIPFVFTKWLQEVFDVPLVIELTDDEKFLFKHKLTINDVKNFARENAKDIIAVGFDPKNTFIFSDLQYMGGAFYETVVRVSRQITGSTAKAVFGFNDSDCIGKFHFASIQIATAFPSSFPNVLGLPDKTPCLIPCAIDQDPYFRVCRDVADKLKYSKPALLHSRFFPALQGSTTKMSASDDTTAIFMTDTPKQIQKKINKYAFSGGQVSADLHRELGGNPDVDVAYQYLSFFKDDDVFLKECYDKYKSGELLSGEMKKLCIETLQEFVKAFQERRAQVDEETLDKFMVPHKLVWGEKERLVAPKP 425
               SCOP domains d3kt8c_ C: Tryptophanyl-tRNA synthetase (TrpRS)                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....ee............hhhhhhhhhh.ee.hhhhhhhhhhhhh...hhhhhh..eeeeehhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhh...hhhhhhhhhhhhhhhhhh.......eeeeehhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...........eeeeee..hhhhhhhhhhhhhhh.....eeeee..........................hhhhhhhhhhhhh......hhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------AA_TRNA_LIG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:23-425 UniProt: 1-432 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                 Transcript 1
                 3kt8 C  23 KEQVVTPWDVEGGVDEQGRAQNIDYDKLIKQFGTKPVNEETLKRFKQVTGREPHHFLRKGLFFSERDFTKILDLYEQGKPFFLYTGRGPSSDSMHLGHMIPFVFTKWLQEVFDVPLVIELTDDEKFLFKHKLTINDVKNFARENAKDIIAVGFDPKNTFIFSDLQYMGGAFYETVVRVSRQITGSTAKAVFGFNDSDCIGKFHFASIQIATAFPSSFPNVLGLPDKTPCLIPCAIDQDPYFRVCRDVADKLKYSKPALLHSRFFPALQGSTTKMSASDDTTAIFMTDTPKQIQKKINKYAFSGGQVSADLHRELGGNPDVDVAYQYLSFFKDDDVFLKECYDKYKSGELLSGEMKKLCIETLQEFVKAFQERRAQVDEETLDKFMVPHKLVWGEKERLVAPKP 425
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422

Chain D from PDB  Type:PROTEIN  Length:410
 aligned with SYWC_YEAST | Q12109 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:410
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425
           SYWC_YEAST    16 ELKSTDVKEQVVTPWDVEGGVDEQGRAQNIDYDKLIKQFGTKPVNEETLKRFKQVTGREPHHFLRKGLFFSERDFTKILDLYEQGKPFFLYTGRGPSSDSMHLGHMIPFVFTKWLQEVFDVPLVIELTDDEKFLFKHKLTINDVKNFARENAKDIIAVGFDPKNTFIFSDLQYMGGAFYETVVRVSRQITGSTAKAVFGFNDSDCIGKFHFASIQIATAFPSSFPNVLGLPDKTPCLIPCAIDQDPYFRVCRDVADKLKYSKPALLHSRFFPALQGSTTKMSASDDTTAIFMTDTPKQIQKKINKYAFSGGQVSADLHRELGGNPDVDVAYQYLSFFKDDDVFLKECYDKYKSGELLSGEMKKLCIETLQEFVKAFQERRAQVDEETLDKFMVPHKLVWGEKERLVAPKP 425
               SCOP domains d3kt8d_ D: Tryptophanyl-tRNA synthetase (TrpRS)                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tRNA-synt_1b-3kt8D01 D:246-389                                                                                                                  ------------------------------------ Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tRNA-synt_1b-3kt8D02 D:246-389                                                                                                                  ------------------------------------ Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tRNA-synt_1b-3kt8D03 D:246-389                                                                                                                  ------------------------------------ Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tRNA-synt_1b-3kt8D04 D:246-389                                                                                                                  ------------------------------------ Pfam domains (4)
           Pfam domains (5) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tRNA-synt_1b-3kt8D05 D:246-389                                                                                                                  ------------------------------------ Pfam domains (5)
           Pfam domains (6) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tRNA-synt_1b-3kt8D06 D:246-389                                                                                                                  ------------------------------------ Pfam domains (6)
           Pfam domains (7) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tRNA-synt_1b-3kt8D07 D:246-389                                                                                                                  ------------------------------------ Pfam domains (7)
           Pfam domains (8) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tRNA-synt_1b-3kt8D08 D:246-389                                                                                                                  ------------------------------------ Pfam domains (8)
         Sec.struct. author ..........eee..eee..ee..ee....hhhhhhhhhh.ee.hhhhhhhhhhhhh...hhhhhh..eeeeehhhhhhhhhhh....eeeeee.......hhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhh...hhhhhhhhhhhhhhhhhh.......eeeeehhhhhhhhhhhhhhhhhh..hhhhhhhhh......hhhhhhhhhhhhhhhhhhhh...........eeeeee..hhhhhhhhhhhhh.......eeeee..........................hhhhhhhhhhhhh......hhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------AA_TRNA_LIG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:16-425 UniProt: 1-432 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                        Transcript 1
                 3kt8 D  16 ELKSTDVKEQVVTPWDVEGGVDEQGRAQNIDYDKLIKQFGTKPVNEETLKRFKQVTGREPHHFLRKGLFFSERDFTKILDLYEQGKPFFLYTGRGPSSDSMHLGHMIPFVFTKWLQEVFDVPLVIELTDDEKFLFKHKLTINDVKNFARENAKDIIAVGFDPKNTFIFSDLQYMGGAFYETVVRVSRQITGSTAKAVFGFNDSDCIGKFHFASIQIATAFPSSFPNVLGLPDKTPCLIPCAIDQDPYFRVCRDVADKLKYSKPALLHSRFFPALQGSTTKMSASDDTTAIFMTDTPKQIQKKINKYAFSGGQVSADLHRELGGNPDVDVAYQYLSFFKDDDVFLKECYDKYKSGELLSGEMKKLCIETLQEFVKAFQERRAQVDEETLDKFMVPHKLVWGEKERLVAPKP 425
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425

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 '\|'

(no "CATH Domain" information available for 3KT8)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HUP (230)

Family: tRNA-synt_1b (51)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (4)

1a	tRNA-synt_1b-3kt8D01	D:246-389
1b	tRNA-synt_1b-3kt8D02	D:246-389
1c	tRNA-synt_1b-3kt8D03	D:246-389
1d	tRNA-synt_1b-3kt8D04	D:246-389
1e	tRNA-synt_1b-3kt8D05	D:246-389
1f	tRNA-synt_1b-3kt8D06	D:246-389
1g	tRNA-synt_1b-3kt8D07	D:246-389
1h	tRNA-synt_1b-3kt8D08	D:246-389

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (SYWC_YEAST | Q12109)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	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:0004830	tryptophan-tRNA ligase activity	Catalysis of the reaction: ATP + L-tryptophan + tRNA(Trp) = AMP + diphosphate + L-tryptophanyl-tRNA(Trp).
biological process
	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: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.
	GO:0006436	tryptophanyl-tRNA aminoacylation	The process of coupling tryptophan to tryptophanyl-tRNA, catalyzed by tryptophanyl-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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3kt8)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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 ](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)

Access by PDB/NDB ID
	3kt8
		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
	SYWC_YEAST \| Q12109
		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)
	6.1.1.2
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

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	(no 'MIM ID' available)
		Disease Information	:	OMIM

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	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

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
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Access by UniProt ID/Accession number
	SYWC_YEAST \| Q12109
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	SYWC_YEAST \| Q12109	:	2ip1 3kt0 3kt3 3kt6

3kt0	THE SAME PROTEIN IN APO FORM
3kt3	THE SAME PROTEIN IN COMPLEX WITH TRPAMP
3kt6	THE SAME PROTEIN IN COMPLEX WITH TRP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 14)

Sites (14, 14)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (1, 4)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (1, 8)

Gene Ontology (9, 9)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File