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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF THE D-ALANYL-ALANINE SYNTHETASE A FROM SALMONELLA ENTERICA TYPHIMURIUM COMPLEXED WITH ADP

Authors :   R. Zhang, N. Maltseva, L. Papazisi, W. Anderson, A. Joachimiak, Center Structural Genomics Of Infectious Diseases (Csgid)

Date :   17 Dec 10 (Deposition) - 12 Jan 11 (Release) - 12 Jan 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Alpha Beta Sandwich, Cytosol, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Zhang, N. Maltseva, L. Papazisi, W. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)
The Crystal Structure Of The D-Alanyl-Alanine Synthetase A From Salmonella Enterica Typhimurium Complexed With Adp
To Be Published
PubMed: search

Molecule 1 - D-ALANINE--D-ALANINE LIGASE A
	Chains	:	A, B, C, D
	EC Number	:	6.3.2.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG19C
	Expression System Strain	:	BL21MAGIC
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DDL, DDLA, STM0380
	Organism Scientific	:	SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
	Organism Taxid	:	90371
	Strain	:	LT2
	Synonym	:	D-ALA-D-ALA LIGASE A, D-ALANYLALANINE SYNTHETASE A

		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 (6, 34)

No.	Name	Count	Type	Full Name
1	ADP	4	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	FMT	5	Ligand/Ion	FORMIC ACID
3	GOL	4	Ligand/Ion	GLYCEROL
4	MG	3	Ligand/Ion	MAGNESIUM ION
5	MSE	17	Mod. Amino Acid	SELENOMETHIONINE
6	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (5, 17)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	FMT	4	Ligand/Ion	FORMIC ACID
3	GOL	2	Ligand/Ion	GLYCEROL
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
6	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (4, 14)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	FMT	1	Ligand/Ion	FORMIC ACID
3	GOL	2	Ligand/Ion	GLYCEROL
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
6	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:141 , PHE A:183 , LYS A:185 , GLY A:190 , SER A:191 , SER A:192 , GLU A:221 , GLN A:222 , GLY A:223 , ILE A:224 , GLU A:228 , LEU A:249 , PHE A:304 , ASN A:314 , GLU A:315 , MG A:372 , HOH A:494	BINDING SITE FOR RESIDUE ADP A 370
02	AC2	SOFTWARE	PRO A:126 , PHE A:127 , ALA A:350 , ARG A:353 , HIS A:354	BINDING SITE FOR RESIDUE FMT A 371
03	AC3	SOFTWARE	GLU A:315 , ADP A:370 , HOH A:493 , HOH A:494 , HOH A:495	BINDING SITE FOR RESIDUE MG A 372
04	AC4	SOFTWARE	ASN A:236 , ASP A:237 , CYS A:295 , ALA A:296 , ARG A:353 , HOH A:375 , HOH A:383	BINDING SITE FOR RESIDUE GOL A 373
05	AC5	SOFTWARE	LYS B:141 , PHE B:183 , LYS B:185 , GLY B:190 , SER B:191 , SER B:192 , GLU B:221 , GLN B:222 , GLY B:223 , ILE B:224 , GLU B:228 , PHE B:304 , ASN B:314 , GLU B:315 , MG B:371	BINDING SITE FOR RESIDUE ADP B 370
06	AC6	SOFTWARE	ASP B:302 , GLU B:315 , ADP B:370	BINDING SITE FOR RESIDUE MG B 371
07	AC7	SOFTWARE	GLN B:240 , ARG B:345	BINDING SITE FOR RESIDUE FMT B 372
08	AC8	SOFTWARE	HIS B:85 , GLN B:86 , LEU B:87 , LEU B:96 , PRO B:97 , THR B:98 , VAL B:99	BINDING SITE FOR RESIDUE FMT B 373
09	AC9	SOFTWARE	ASN B:236 , CYS B:295 , ALA B:296	BINDING SITE FOR RESIDUE FMT B 374
10	BC1	SOFTWARE	ARG B:300 , GLY B:321 , SER B:326 , MSE B:327 , HOH B:365 , HOH B:415	BINDING SITE FOR RESIDUE SO4 B 375
11	BC2	SOFTWARE	CYS B:138 , MSE B:139 , LYS B:141 , ALA B:187 , GLN B:189 , GLU B:315 , ILE B:316 , ASN B:317 , HOH B:386	BINDING SITE FOR RESIDUE GOL B 376
12	BC3	SOFTWARE	PHE C:183 , LYS C:185 , GLY C:190 , SER C:191 , SER C:192 , GLU C:221 , GLN C:222 , GLY C:223 , ILE C:224 , GLU C:228 , PHE C:304 , ASN C:314 , GLU C:315	BINDING SITE FOR RESIDUE ADP C 370
13	BC4	SOFTWARE	ARG C:300 , GLY C:321 , SER C:326 , MSE C:327 , HOH C:416	BINDING SITE FOR RESIDUE GOL C 371
14	BC5	SOFTWARE	PRO C:126 , PHE C:127 , ALA C:350 , ARG C:353 , HIS C:354 , HOH C:397	BINDING SITE FOR RESIDUE GOL C 372
15	BC6	SOFTWARE	LYS D:141 , PHE D:183 , LYS D:185 , GLN D:189 , GLY D:190 , SER D:191 , SER D:192 , GLU D:221 , GLN D:222 , GLY D:223 , ILE D:224 , GLU D:228 , LEU D:249 , PHE D:304 , ASN D:314 , GLU D:315 , MG D:372 , HOH D:470	BINDING SITE FOR RESIDUE ADP D 370
16	BC7	SOFTWARE	PRO D:126 , PHE D:127 , ALA D:350 , ARG D:353 , HIS D:354 , HOH D:469	BINDING SITE FOR RESIDUE FMT D 371
17	BC8	SOFTWARE	GLU D:315 , ADP D:370 , HOH D:470 , HOH D:471 , HOH D:472	BINDING SITE FOR RESIDUE MG D 372

(no "SS Bond" information available for 3Q1K)

Asymmetric Unit

No.	Residues
1	Leu A:180	-	Pro A:181
2	Val A:270	-	Pro A:271
3	Leu B:180	-	Pro B:181
4	Val B:270	-	Pro B:271
5	Leu C:180	-	Pro C:181
6	Val C:270	-	Pro C:271
7	Leu D:180	-	Pro D:181
8	Val D:270	-	Pro D:271

Asymmetric Unit (1, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_DDLA_SALTY_001 *	H	17	A	DDLA_SALTY	---	---	A/B/C/D	H	17	A
	* ID not provided by source

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

Biological Unit 1 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_DDLA_SALTY_001 *	H	17	A	DDLA_SALTY	---	---	A/B	H	17	A
	* ID not provided by source

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

Biological Unit 2 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_DDLA_SALTY_001 *	H	17	A	DDLA_SALTY	---	---	C/D	H	17	A
	* ID not provided by source

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

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DALA_DALA_LIGASE_1	PS00843	D-alanine--D-alanine ligase signature 1.	DDLA_SALTY	107-118	4	A:107-118 B:107-118 C:107-118 D:107-118
2	DALA_DALA_LIGASE_2	PS00844	D-alanine--D-alanine ligase signature 2.	DDLA_SALTY	293-321	4	A:293-321 B:293-321 C:293-321 D:293-321

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DALA_DALA_LIGASE_1	PS00843	D-alanine--D-alanine ligase signature 1.	DDLA_SALTY	107-118	2	A:107-118 B:107-118 - -
2	DALA_DALA_LIGASE_2	PS00844	D-alanine--D-alanine ligase signature 2.	DDLA_SALTY	293-321	2	A:293-321 B:293-321 - -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DALA_DALA_LIGASE_1	PS00843	D-alanine--D-alanine ligase signature 1.	DDLA_SALTY	107-118	2	- - C:107-118 D:107-118
2	DALA_DALA_LIGASE_2	PS00844	D-alanine--D-alanine ligase signature 2.	DDLA_SALTY	293-321	2	- - C:293-321 D:293-321

(no "Exon" information available for 3Q1K)

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:357
 aligned with DDLA_SALTY | P0A1F0 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:362
                                    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  
           DDLA_SALTY     2 AKLRVGIVFGGKSAEHEVSLQSAKNIVDAIDKTRFDVVLLGIDKAGQWHVNDAENYLQNADDPAHIALRPSAISLAQVPGKHQHQLINAQNGQPLPTVDVIFPIVHGTLGEDGSLQGMLRVANLPFVGSDVLSSAACMDKDVAKRLLRDAGLNIAPFITLTRTNRHAFSFAEVESRLGLPLFVKPANQGSSVGVSKVANEAQYQQAVALAFEFDHKVVVEQGIKGREIECAVLGNDNPQASTCGEIVLNSEFYAYDTKYIDDNGAQVVVPAQIPSEVNDKIRAIAIQAYQTLGCAGMARVDVFLTADNEVVINEINTLPGFTNISMYPKLWQASGLGYTDLISRLIELALERHTANNALKTT 363
               SCOP domains d3q1ka1 A:2-139 automated matches                                                                                                         d3q1ka2 A:140-363 automated matches                                                                                                                                                                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....hhhhhhhhhhhhhhhh....eeeeeeee.....eeee.....ee........ee......eee........eee...........eeee.........hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh......eeee........hhhhhhhhhh..eeeee.........eee.hhhhhhhhhhhhh.....eeeee....eeeeeeeee....eeeeeeeee.....-----..hhhhhheee.....hhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeee........hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------A---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------DALA_DALA_LI------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2           ------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q1k A   2 AKLRVGIVFGGKSAEHEVSLQSAKNIVDAIDKTRFDVVLLGIDKAGQWHVNDAENYLQNADDPAHIALRPSAISLAQVPGKHQHQLINAQNGQPLPTVDVIFPIVHGTLGEDGSLQGmLRVANLPFVGSDVLSSAACmDKDVAKRLLRDAGLNIAPFITLTRTNRHAFSFAEVESRLGLPLFVKPANQGSSVGVSKVANEAQYQQAVALAFEFDHKVVVEQGIKGREIECAVLGNDNPQASTCGEIVLNSEF-----KYIDDNGAQVVVPAQIPSEVNDKIRAIAIQAYQTLGCAGmARVDVFLTADNEVVINEINTLPGFTNISmYPKLWQASGLGYTDLISRLIELALERHTANNALKTT 363
                                    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  
                                                                                                                                               119-MSE             139-MSE                                                                                                           253   259                                    298-MSE                      327-MSE

Chain B from PDB  Type:PROTEIN  Length:346
 aligned with DDLA_SALTY | P0A1F0 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:362
                                    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  
           DDLA_SALTY     2 AKLRVGIVFGGKSAEHEVSLQSAKNIVDAIDKTRFDVVLLGIDKAGQWHVNDAENYLQNADDPAHIALRPSAISLAQVPGKHQHQLINAQNGQPLPTVDVIFPIVHGTLGEDGSLQGMLRVANLPFVGSDVLSSAACMDKDVAKRLLRDAGLNIAPFITLTRTNRHAFSFAEVESRLGLPLFVKPANQGSSVGVSKVANEAQYQQAVALAFEFDHKVVVEQGIKGREIECAVLGNDNPQASTCGEIVLNSEFYAYDTKYIDDNGAQVVVPAQIPSEVNDKIRAIAIQAYQTLGCAGMARVDVFLTADNEVVINEINTLPGFTNISMYPKLWQASGLGYTDLISRLIELALERHTANNALKTT 363
               SCOP domains d3q1kb1 B:2-139 automated matches                                                                                                         d3q1kb2 B:140-363 automated matches                                                                                                                                                                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....hhhhhhhhhhhhhhhh....eeeeeeee.....eeee.....ee........ee......eee........eee...........eeee.........hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh......eeeee.......hhhhhhhhhh..eeeee.........eee.hhhhhhhhhhhhh....eeeeee....eeeeeeeee....eeeeeeeee.----------------.eee.....hhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeee........hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------A---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------DALA_DALA_LI------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2           ------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q1k B   2 AKLRVGIVFGGKSAEHEVSLQSAKNIVDAIDKTRFDVVLLGIDKAGQWHVNDAENYLQNADDPAHIALRPSAISLAQVPGKHQHQLINAQNGQPLPTVDVIFPIVHGTLGEDGSLQGmLRVANLPFVGSDVLSSAACmDKDVAKRLLRDAGLNIAPFITLTRTNRHAFSFAEVESRLGLPLFVKPANQGSSVGVSKVANEAQYQQAVALAFEFDHKVVVEQGIKGREIECAVLGNDNPQASTCGEIVL----------------AQVVVPAQIPSEVNDKIRAIAIQAYQTLGCAGmARVDVFLTADNEVVINEINTLPGFTNISmYPKLWQASGLGYTDLISRLIELALERHTANNALKTT 363
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       | -         -    |  271       281       291      |301       311       321     | 331       341       351       361  
                                                                                                                                               119-MSE             139-MSE                                                                                                       249              266                             298-MSE                      327-MSE

Chain C from PDB  Type:PROTEIN  Length:345
 aligned with DDLA_SALTY | P0A1F0 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:363
                                    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   
           DDLA_SALTY     2 AKLRVGIVFGGKSAEHEVSLQSAKNIVDAIDKTRFDVVLLGIDKAGQWHVNDAENYLQNADDPAHIALRPSAISLAQVPGKHQHQLINAQNGQPLPTVDVIFPIVHGTLGEDGSLQGMLRVANLPFVGSDVLSSAACMDKDVAKRLLRDAGLNIAPFITLTRTNRHAFSFAEVESRLGLPLFVKPANQGSSVGVSKVANEAQYQQAVALAFEFDHKVVVEQGIKGREIECAVLGNDNPQASTCGEIVLNSEFYAYDTKYIDDNGAQVVVPAQIPSEVNDKIRAIAIQAYQTLGCAGMARVDVFLTADNEVVINEINTLPGFTNISMYPKLWQASGLGYTDLISRLIELALERHTANNALKTTM 364
               SCOP domains d3q1kc1 C:2-139 automated matches                                                                                                         d3q1kc2 C:140-364 automated matches                                                                                                                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....hhhhhhhhhhhhhhhh....eeeeeeee.....eeee.....ee........ee......eee........eee...........eeee.........hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh......eeeee.......hhhhhhhhhh..eeeee.........eee.hhhhhhhhhhhhh....eeeeee....eeeeeeee.....eeeeeeee..------------------.......hhhhhhhhhhhhhhhhhhh....eeeeeeee.....eeeeeee........hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------A----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------DALA_DALA_LI------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2           ------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q1k C   2 AKLRVGIVFGGKSAEHEVSLQSAKNIVDAIDKTRFDVVLLGIDKAGQWHVNDAENYLQNADDPAHIALRPSAISLAQVPGKHQHQLINAQNGQPLPTVDVIFPIVHGTLGEDGSLQGmLRVANLPFVGSDVLSSAACmDKDVAKRLLRDAGLNIAPFITLTRTNRHAFSFAEVESRLGLPLFVKPANQGSSVGVSKVANEAQYQQAVALAFEFDHKVVVEQGIKGREIECAVLGNDNPQASTCGEIVL------------------VVVPAQIPSEVNDKIRAIAIQAYQTLGCAGmARVDVFLTADNEVVINEINTLPGFTNISmYPKLWQASGLGYTDLISRLIELALERHTANNALKTTm 364
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       | -         -      |271       281       291      |301       311       321     | 331       341       351       361  |
                                                                                                                                               119-MSE             139-MSE                                                                                                       249                268                           298-MSE                      327-MSE                              364-MSE

Chain D from PDB  Type:PROTEIN  Length:355
 aligned with DDLA_SALTY | P0A1F0 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:361
                                    12        22        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 
           DDLA_SALTY     3 KLRVGIVFGGKSAEHEVSLQSAKNIVDAIDKTRFDVVLLGIDKAGQWHVNDAENYLQNADDPAHIALRPSAISLAQVPGKHQHQLINAQNGQPLPTVDVIFPIVHGTLGEDGSLQGMLRVANLPFVGSDVLSSAACMDKDVAKRLLRDAGLNIAPFITLTRTNRHAFSFAEVESRLGLPLFVKPANQGSSVGVSKVANEAQYQQAVALAFEFDHKVVVEQGIKGREIECAVLGNDNPQASTCGEIVLNSEFYAYDTKYIDDNGAQVVVPAQIPSEVNDKIRAIAIQAYQTLGCAGMARVDVFLTADNEVVINEINTLPGFTNISMYPKLWQASGLGYTDLISRLIELALERHTANNALKTT 363
               SCOP domains d3q1kd1 D:3-139 automated matches                                                                                                        d3q1kd2 D:140-363 automated matches                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Dala_Dala_lig_N-3q1kD05 D:4-130                                                                                                ----------------Dala_Dala_lig_C-3q1kD01 D:147-348                                                                                                                                                                         --------------- Pfam domains (1)
           Pfam domains (2) -Dala_Dala_lig_N-3q1kD06 D:4-130                                                                                                ----------------Dala_Dala_lig_C-3q1kD02 D:147-348                                                                                                                                                                         --------------- Pfam domains (2)
           Pfam domains (3) -Dala_Dala_lig_N-3q1kD07 D:4-130                                                                                                ----------------Dala_Dala_lig_C-3q1kD03 D:147-348                                                                                                                                                                         --------------- Pfam domains (3)
           Pfam domains (4) -Dala_Dala_lig_N-3q1kD08 D:4-130                                                                                                ----------------Dala_Dala_lig_C-3q1kD04 D:147-348                                                                                                                                                                         --------------- Pfam domains (4)
         Sec.struct. author .eeeeeeee....hhhhhhhhhhhhhhhh....eeeeeeee.....eeee.....ee........ee......eee........eee...........eeee.........hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh......eeeee.......hhhhhhhhhh..eeeee.........eee.hhhhhhhhhhhhh....eeeeee....eeeeeeeee....eeeeeeeee.....------.hhhhhheee.....hhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeee........hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------A---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------DALA_DALA_LI------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2           ------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q1k D   3 KLRVGIVFGGKSAEHEVSLQSAKNIVDAIDKTRFDVVLLGIDKAGQWHVNDAENYLQNADDPAHIALRPSAISLAQVPGKHQHQLINAQNGQPLPTVDVIFPIVHGTLGEDGSLQGmLRVANLPFVGSDVLSSAACmDKDVAKRLLRDAGLNIAPFITLTRTNRHAFSFAEVESRLGLPLFVKPANQGSSVGVSKVANEAQYQQAVALAFEFDHKVVVEQGIKGREIECAVLGNDNPQASTCGEIVLNSEF------YIDDNGAQVVVPAQIPSEVNDKIRAIAIQAYQTLGCAGmARVDVFLTADNEVVINEINTLPGFTNISmYPKLWQASGLGYTDLISRLIELALERHTANNALKTT 363
                                    12        22        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 
                                                                                                                                              119-MSE             139-MSE                                                                                                           253    260                                   298-MSE                      327-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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: ATP-grasp (191)

Superfamily: Glutathione synthetase ATP-binding domain-like (158)

Family: automated matches (42)

Protein domain: automated matches (42)

Salmonella enterica [TaxId: 90371] (1)

1a	d3q1ka2	A:140-363
1b	d3q1kb2	B:140-363
1c	d3q1kc2	C:140-364
1d	d3q1kd2	D:140-363

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

Fold: PreATP-grasp domain (131)

Superfamily: PreATP-grasp domain (131)

Family: automated matches (45)

Protein domain: automated matches (45)

Salmonella enterica [TaxId: 90371] (1)

2a	d3q1ka1	A:2-139
2b	d3q1kb1	B:2-139
2c	d3q1kc1	C:2-139
2d	d3q1kd1	D:3-139

(no "CATH Domain" information available for 3Q1K)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: ATP-grasp (83)

Family: Dala_Dala_lig_C (12)

Salmonella typhimurium (1)

1a	Dala_Dala_lig_C-3q1kD01	D:147-348
1b	Dala_Dala_lig_C-3q1kD02	D:147-348
1c	Dala_Dala_lig_C-3q1kD03	D:147-348
1d	Dala_Dala_lig_C-3q1kD04	D:147-348

Clan: no clan defined [family: Dala_Dala_lig_N] (12)

Family: Dala_Dala_lig_N (12)

Salmonella typhimurium (1)

2a	Dala_Dala_lig_N-3q1kD05	D:4-130
2b	Dala_Dala_lig_N-3q1kD06	D:4-130
2c	Dala_Dala_lig_N-3q1kD07	D:4-130
2d	Dala_Dala_lig_N-3q1kD08	D:4-130

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (DDLA_SALTY | P0A1F0)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0008716	D-alanine-D-alanine ligase activity	Catalysis of the reaction: 2 D-alanine + ATP = D-alanyl-D-alanine + ADP + 2 H(+) + phosphate.
	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: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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
biological process
	GO:0071555	cell wall organization	A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
	GO:0009252	peptidoglycan biosynthetic process	The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
	GO:0008360	regulation of cell shape	Any process that modulates the surface configuration of a cell.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	3q1k
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UniProtKB/Swiss-Prot
	DDLA_SALTY \| P0A1F0	:	3i12

3i12	SAME PROTEIN WITHOUT LIGAND RELATED ID: IDP00919 RELATED DB: TARGETDB

Description

Compounds

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Ligands, Modified Residues, Ions (6, 34)

Sites (17, 17)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

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